GET /v3/datasets?format=api&offset=240
HTTP 200 OK
Allow: GET, POST, OPTIONS
Content-Type: application/json
Vary: Accept

{
    "count": 7415,
    "next": "https://metax.fairdata.fi/v3/datasets?format=api&limit=20&offset=260",
    "previous": "https://metax.fairdata.fi/v3/datasets?format=api&limit=20&offset=220",
    "results": [
        {
            "id": "cd24b732-a37a-4c3f-9c30-b0d10c123855",
            "access_rights": {
                "id": "2099a978-a957-4316-831a-efda77860484",
                "license": [
                    {
                        "id": "35b18e72-3819-4ec6-a1be-14624f29d968",
                        "url": "http://uri.suomi.fi/codelist/fairdata/license/code/CC-BY-4.0",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/license",
                        "pref_label": {
                            "en": "Creative Commons Attribution 4.0 International (CC BY 4.0)",
                            "fi": "Creative Commons Nimeä 4.0 Kansainvälinen (CC BY 4.0)"
                        }
                    }
                ],
                "access_type": {
                    "id": "d01ac02c-fc70-4c68-9434-8383cb693ff0",
                    "url": "http://uri.suomi.fi/codelist/fairdata/access_type/code/open",
                    "in_scheme": "http://uri.suomi.fi/codelist/fairdata/access_type",
                    "pref_label": {
                        "en": "Open",
                        "fi": "Avoin"
                    }
                },
                "restriction_grounds": []
            },
            "actors": [
                {
                    "id": "f919c16a-7ee6-4cc3-b03f-de78c7c2af0e",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "a93330c6-aee5-450e-8fec-17c7f78ec07d",
                        "name": "Gautier Follain"
                    },
                    "organization": {
                        "id": "05f54298-88f3-4860-85eb-2476cf4d2e5d",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "631251a8-7381-4a76-ad6b-911cd4f3861d",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "9a34ac10-bfa9-4c72-81d1-979b69119dc8",
                        "name": "Sujan Ghimire",
                        "external_identifier": "https://orcid.org/0000-0003-3660-4300"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "e3dc0b31-12aa-44fb-bcd2-5d70bdb00e8a",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "32f8c97e-f007-4bc2-8746-5ba3a5f344d2",
                        "name": "Joanna Pylvänäinen",
                        "external_identifier": "https://orcid.org/0000-0002-3540-5150"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "36b3acf6-b285-4407-ae71-64f39ddcb152",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "1218ba4b-7531-4690-b045-f4c7ad0c51e4",
                        "name": "Johanna Ivaska"
                    },
                    "organization": {
                        "id": "05f54298-88f3-4860-85eb-2476cf4d2e5d",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "7be1bdca-5aba-4e1b-9102-3eb7669af596",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "2deada53-0534-4284-9ae9-3aa1f75f37f9",
                        "name": "Guillaume Jacquemet",
                        "external_identifier": "https://orcid.org/0000-0002-9286-920X"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "c79da936-ea9e-4ffc-aa9c-38571b52e842",
                    "roles": [
                        "publisher"
                    ],
                    "organization": {
                        "id": "adb16083-c73d-4150-a576-733d2d7a86c9",
                        "pref_label": {
                            "en": "Zenodo",
                            "fi": "Zenodo",
                            "sv": "Zenodo"
                        }
                    }
                }
            ],
            "cumulative_state": 0,
            "data_catalog": "urn:nbn:fi:att:data-catalog-abo",
            "description": {
                "en": "This dataset contains tracking results of different combinations of Hyaluronidase-treated AsPC1 and MiaPaca cells perfused on Hyaluronidase-treated endothelial monolayer under physiological flow speeds. Videos were recorded using a Nikon Eclipse Ti2-E microscope and 20x objective. Perfused cells from the generated videos were segmented using custom-trained Stardist models. Tracking was performed using TrackMate, and tracking results were analyzed using a custom CellTracksColab notebook. The dataset here contains the CSV files generated by TrackMate (Track and Spots information), the tracking data stored in the CellTracksColab format (Analysis.zip), and the analysis output used in the paper (Analysis.zip). Sample information AsPC1 and MiaPaca cells perfused on HUVEC cells under physiological flow speeds: 400 µm/s (p1), 200 µm/s (p2), 100 µm/s (p3) and 400 µm/s (p4). Hyaluronidase treatment PDACs or HUVECs prior to perfusion Imaging specs Microscope: Nikon Eclipse Ti2-E, 20x objective Data Type: Brightfield microscopy images (16-bit) Image Size: 1024 x 1022 pixels (Pixel size: 650 nm) Recording speed 25 frames/s DL models: Cancer cells: https://doi.org/10.5281/zenodo.10572122 Neutrophils: https://doi.org/10.5281/zenodo.10572231 Mononucleated cells: https://doi.org/10.5281/zenodo.10572200 Model Training and predictions: Conducted using ZeroCostDL4Mic (https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki) Tracking parameters (TrackMate): Detection: label detector Tracking: Simple LAP detector: Linking max distance: 20 px; Gap-closing max distance: 20 px; Gap-closing max frame gap: 4. Track filtering: min number of spots in the tracks 11.79 Tracking analysis Tracks were analyzed using a customized CellTracksColab notebook (https://github.com/CellMigrationLab/PDAC_DL/tree/main/CellTracksColab) Contents of the repository Analysis.zip dataset As_ctrl.zip As_HUdigestion.zip As_TCdigestion.zip Mia_ctrl.zip Mia_HUdig.zip Mia_TCdig.zip Reference Biorxiv paper"
            },
            "field_of_science": [
                {
                    "id": "e9745cdf-d0e1-4797-8fee-3324e5b2bee2",
                    "url": "http://www.yso.fi/onto/okm-tieteenala/ta1182",
                    "in_scheme": "http://www.yso.fi/onto/okm-tieteenala/conceptscheme",
                    "pref_label": {
                        "en": "Biochemistry, cell and molecular biology",
                        "fi": "Biokemia, solu- ja molekyylibiologia",
                        "sv": "Biokemi, cell- och molekylärbiologi"
                    }
                }
            ],
            "infrastructure": [],
            "issued": "2024-09-02",
            "keyword": [
                "Biochemistry and Cell Biology",
                "cells",
                "endothelial monolayer"
            ],
            "language": [],
            "metadata_owner": {
                "id": "dde6b62a-99e9-49c2-92bc-4a08ae3d9a09",
                "organization": "service_abo"
            },
            "other_identifiers": [],
            "persistent_identifier": "doi:10.5281/zenodo.13627037",
            "pid_generated_by_fairdata": false,
            "projects": [],
            "provenance": [],
            "relation": [],
            "remote_resources": [],
            "spatial": [],
            "state": "published",
            "temporal": [],
            "theme": [],
            "title": {
                "en": "Hyaluronidase treatment perfusion tracking dataset"
            },
            "created": "2025-03-17T05:58:03Z",
            "modified": "2025-03-17T05:58:03Z",
            "dataset_versions": [
                {
                    "id": "cd24b732-a37a-4c3f-9c30-b0d10c123855",
                    "title": {
                        "en": "Hyaluronidase treatment perfusion tracking dataset"
                    },
                    "persistent_identifier": "doi:10.5281/zenodo.13627037",
                    "state": "published",
                    "created": "2025-03-17T05:58:03Z",
                    "version": 1
                }
            ],
            "published_revision": 1,
            "version": 1,
            "api_version": 3,
            "metadata_repository": "Fairdata"
        },
        {
            "id": "3f2e68f2-a8d1-4c4a-a572-c16a8b5fdcf4",
            "access_rights": {
                "id": "37a4529f-2576-4cbd-b716-80e8fa6ee347",
                "license": [
                    {
                        "id": "35b18e72-3819-4ec6-a1be-14624f29d968",
                        "url": "http://uri.suomi.fi/codelist/fairdata/license/code/CC-BY-4.0",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/license",
                        "pref_label": {
                            "en": "Creative Commons Attribution 4.0 International (CC BY 4.0)",
                            "fi": "Creative Commons Nimeä 4.0 Kansainvälinen (CC BY 4.0)"
                        }
                    }
                ],
                "access_type": {
                    "id": "d01ac02c-fc70-4c68-9434-8383cb693ff0",
                    "url": "http://uri.suomi.fi/codelist/fairdata/access_type/code/open",
                    "in_scheme": "http://uri.suomi.fi/codelist/fairdata/access_type",
                    "pref_label": {
                        "en": "Open",
                        "fi": "Avoin"
                    }
                },
                "restriction_grounds": []
            },
            "actors": [
                {
                    "id": "30e82656-3b6c-4ef7-afbd-679a883f32b4",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "314128a7-0fdd-45b1-a286-086b0e7f7390",
                        "name": "Gautier Follain"
                    },
                    "organization": {
                        "id": "657dca2f-6def-4df7-8cde-3c81e0d3c091",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "aa2721cc-a394-41ba-88b7-ed9f0e7a7d50",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "82eba559-2d80-4ae6-a40d-d72399baf901",
                        "name": "Sujan Ghimire",
                        "external_identifier": "https://orcid.org/0000-0003-3660-4300"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "50d6eaa9-a964-4ef1-9b81-9454fb6008c4",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "53275bca-2d70-4ec9-90d1-3f988c8a7551",
                        "name": "Joanna Pylvänäinen",
                        "external_identifier": "https://orcid.org/0000-0002-3540-5150"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "fa1f5bff-b7be-4ccf-a923-cd4e5dad5e7d",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "f1aa14d9-8d87-4155-9952-eb20c9c55394",
                        "name": "Johanna Ivaska"
                    },
                    "organization": {
                        "id": "657dca2f-6def-4df7-8cde-3c81e0d3c091",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "fdfbd87e-257f-4915-9208-1c1fdc6dc7a9",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "af915f70-487c-4a25-b294-ec9f753cbde5",
                        "name": "Guillaume Jacquemet",
                        "external_identifier": "https://orcid.org/0000-0002-9286-920X"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "462c07d6-1c2e-466c-9b7e-aac9cd635f2e",
                    "roles": [
                        "publisher"
                    ],
                    "organization": {
                        "id": "3475e565-841a-4c1a-8063-43900b2781a3",
                        "pref_label": {
                            "en": "Zenodo",
                            "fi": "Zenodo",
                            "sv": "Zenodo"
                        }
                    }
                }
            ],
            "cumulative_state": 0,
            "data_catalog": "urn:nbn:fi:att:data-catalog-abo",
            "description": {
                "en": "This dataset contains tracking results of PDAC (AsPC1, MiaPaca, and Panc10) and immune cells (Mononucleated cells and neutrophils) perfused on endothelial monolayer under physiological flow speeds and with or without IL-1β treatment. Imaged using brightfield microscopy using a Nikon Eclipse Ti2-E microscope and 20x objective. Perfused cells from the generated videos were segmented using custom Stardist models. Tracking was performed using TrackMate, and tracking results were analyzed using a custom CellTracksColab notebook. The dataset here contains the CSV files generated by TrackMate (Track and Spots information), the tracking data stored in the CellTracksColab format (Analysis.zip), and the analysis output used in the paper (Analysis.zip). It also contains the segmented images of the endothelial cell-cell junctions and nuclei (Landmark.zip). Specifications Sample information PDAC (AsPC1, MiaPaca, and Panc10) and immune cells (Mononucleated cells and neutrophils) perfused on HUVEC cells under physiological flow speeds: 400 µm/s (p1), 200 µm/s (p2), 100 µm/s (p3) and 400 µm/s (p4). Control and IL-1β treated (10 µg/ml for 2 h) HUVEC monolayer Imaging specs Microscope: Nikon Eclipse Ti2-E, 20x objective Data Type: Brightfield microscopy images (16-bit) Image Size: 1024 x 1022 pixels (Pixel size: 650 nm) Recording speed 25 frames/s DL models: Cancer cells: https://doi.org/10.5281/zenodo.10572122 Neutrophils: https://doi.org/10.5281/zenodo.10572231 Mononucleated cells: https://doi.org/10.5281/zenodo.10572200 Model Training and predictions: Conducted using ZeroCostDL4Mic (https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki) Tracking parameters (TrackMate): Detection: label detector Tracking: Simple LAP detector Cancer cells: Linking max distance: 15 px; Gap-closing max distance: 15 px; Gap-closing max frame gap: 2. Track filtering: min number of spots in the tracks 7.74 Immune cells: Linking max distance: 15 px; Gap-closing max distance: 15 px; Gap-closing max frame gap: 4. Track filtering: min number of spots in the tracks 11.79 Tracking analysis Tracks were analyzed using a customized CellTracksColab notebook (https://github.com/CellMigrationLab/PDAC_DL/tree/main/CellTracksColab) Contents of the repository Analysis.zip Landmark.zip As_Ctrl.zip As_IL1b.zip Mia_IL1b.zip Mia_Ctrl.zip P10_ctrl.zip P10_IL1b.zip Mon_ctrl.zip mon_IL1b.zip Neu_ctrl.zip neu_IL1b.zip Reference Biorxiv paper"
            },
            "field_of_science": [
                {
                    "id": "e9745cdf-d0e1-4797-8fee-3324e5b2bee2",
                    "url": "http://www.yso.fi/onto/okm-tieteenala/ta1182",
                    "in_scheme": "http://www.yso.fi/onto/okm-tieteenala/conceptscheme",
                    "pref_label": {
                        "en": "Biochemistry, cell and molecular biology",
                        "fi": "Biokemia, solu- ja molekyylibiologia",
                        "sv": "Biokemi, cell- och molekylärbiologi"
                    }
                }
            ],
            "infrastructure": [],
            "issued": "2024-09-03",
            "keyword": [
                "Biochemistry and Cell Biology",
                "cells"
            ],
            "language": [],
            "metadata_owner": {
                "id": "dde6b62a-99e9-49c2-92bc-4a08ae3d9a09",
                "organization": "service_abo"
            },
            "other_identifiers": [],
            "persistent_identifier": "doi:10.5281/zenodo.13643590",
            "pid_generated_by_fairdata": false,
            "projects": [],
            "provenance": [],
            "relation": [],
            "remote_resources": [],
            "spatial": [],
            "state": "published",
            "temporal": [],
            "theme": [],
            "title": {
                "en": "PDAC cells vs Immune cells perfusion tracking dataset"
            },
            "created": "2025-03-17T05:58:00Z",
            "modified": "2025-03-17T05:58:00Z",
            "dataset_versions": [
                {
                    "id": "3f2e68f2-a8d1-4c4a-a572-c16a8b5fdcf4",
                    "title": {
                        "en": "PDAC cells vs Immune cells perfusion tracking dataset"
                    },
                    "persistent_identifier": "doi:10.5281/zenodo.13643590",
                    "state": "published",
                    "created": "2025-03-17T05:58:00Z",
                    "version": 1
                }
            ],
            "published_revision": 1,
            "version": 1,
            "api_version": 3,
            "metadata_repository": "Fairdata"
        },
        {
            "id": "f799b3ca-710f-4a07-8473-490ed47b670c",
            "access_rights": {
                "id": "dae72809-c879-493c-8126-7e3d3278ec25",
                "license": [
                    {
                        "id": "35b18e72-3819-4ec6-a1be-14624f29d968",
                        "url": "http://uri.suomi.fi/codelist/fairdata/license/code/CC-BY-4.0",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/license",
                        "pref_label": {
                            "en": "Creative Commons Attribution 4.0 International (CC BY 4.0)",
                            "fi": "Creative Commons Nimeä 4.0 Kansainvälinen (CC BY 4.0)"
                        }
                    }
                ],
                "access_type": {
                    "id": "d01ac02c-fc70-4c68-9434-8383cb693ff0",
                    "url": "http://uri.suomi.fi/codelist/fairdata/access_type/code/open",
                    "in_scheme": "http://uri.suomi.fi/codelist/fairdata/access_type",
                    "pref_label": {
                        "en": "Open",
                        "fi": "Avoin"
                    }
                },
                "restriction_grounds": []
            },
            "actors": [
                {
                    "id": "ce298bad-0d9d-46dc-b058-147b19dada55",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "f57393dc-9966-4b18-b744-b137ee4c202b",
                        "name": "Gautier Follain"
                    },
                    "organization": {
                        "id": "dcce6f58-fe53-43a1-a777-356a19caa076",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "9495517b-9442-411e-bb67-9f6b2d2911db",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "5b60f198-5b82-4491-89ea-cea1812bfd95",
                        "name": "Sujan Ghimire",
                        "external_identifier": "https://orcid.org/0000-0003-3660-4300"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "8cebd53f-2bea-484e-955e-d681b6544fb8",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "6cad4fc4-d312-4b93-a16a-6574d32c8bea",
                        "name": "Joanna Pylvänäinen",
                        "external_identifier": "https://orcid.org/0000-0002-3540-5150"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "43f17570-bc7c-40f2-9a94-6dea1d31bfb6",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "3d9559f9-d32e-45cd-a63b-0058a65fb843",
                        "name": "Johanna Ivaska"
                    },
                    "organization": {
                        "id": "dcce6f58-fe53-43a1-a777-356a19caa076",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "c9846f9f-91cf-4ae8-9366-5dd44fe147f0",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "3bda1b27-bd9b-40f5-9efb-fdb9d8b72dac",
                        "name": "Guillaume Jacquemet",
                        "external_identifier": "https://orcid.org/0000-0002-9286-920X"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "2f3be63c-7ad0-4786-aea9-e3bfd3bf1efe",
                    "roles": [
                        "publisher"
                    ],
                    "organization": {
                        "id": "0289ea72-ed01-43c4-8041-6e773a91535d",
                        "pref_label": {
                            "en": "Zenodo",
                            "fi": "Zenodo",
                            "sv": "Zenodo"
                        }
                    }
                }
            ],
            "cumulative_state": 0,
            "data_catalog": "urn:nbn:fi:att:data-catalog-abo",
            "description": {
                "en": "This repository contains a StarDist deep learning model and its training and validation datasets designed for segmenting cancer cells perfused over an endothelial cell monolayer captured at 20x magnification. Using computational methods, the initial dataset of 20 manually annotated images was augmented to 160 paired images. The model was trained over 400 epochs and achieved an average F1 Score of 0.921, demonstrating high accuracy in cell segmentation tasks. Specifications Model: StarDist for cancer cell segmentation on endothelial cells (20x magnification) Training Dataset: Number of Original Images: 20 paired brightfield microscopy images and label masks Microscope: Nikon Eclipse Ti2-E, 20x objective Data Type: Brightfield microscopy images with manually segmented masks File Format: TIFF (.tif) Brightfield Images: 16-bit Masks: 8-bit Image Size: 1024 x 1022 pixels (Pixel size: 650 nm) Training Parameters: Epochs: 400 Patch Size: 992 x 992 pixels Batch Size: 2 Performance: Average F1 Score: 0.921 Average IoU: 0.793 Model Training: Conducted using ZeroCostDL4Mic (https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki) Reference Biorxiv paper"
            },
            "field_of_science": [
                {
                    "id": "e9745cdf-d0e1-4797-8fee-3324e5b2bee2",
                    "url": "http://www.yso.fi/onto/okm-tieteenala/ta1182",
                    "in_scheme": "http://www.yso.fi/onto/okm-tieteenala/conceptscheme",
                    "pref_label": {
                        "en": "Biochemistry, cell and molecular biology",
                        "fi": "Biokemia, solu- ja molekyylibiologia",
                        "sv": "Biokemi, cell- och molekylärbiologi"
                    }
                }
            ],
            "infrastructure": [],
            "issued": "2024-01-26",
            "keyword": [
                "Biochemistry and Cell Biology",
                "cells"
            ],
            "language": [],
            "metadata_owner": {
                "id": "dde6b62a-99e9-49c2-92bc-4a08ae3d9a09",
                "organization": "service_abo"
            },
            "other_identifiers": [],
            "persistent_identifier": "doi:10.5281/zenodo.10572122",
            "pid_generated_by_fairdata": false,
            "projects": [],
            "provenance": [],
            "relation": [],
            "remote_resources": [],
            "spatial": [],
            "state": "published",
            "temporal": [],
            "theme": [],
            "title": {
                "en": "StarDist_BF_cancer_cell_dataset_20x"
            },
            "created": "2025-03-17T05:57:58Z",
            "modified": "2025-03-17T05:57:58Z",
            "dataset_versions": [
                {
                    "id": "f799b3ca-710f-4a07-8473-490ed47b670c",
                    "title": {
                        "en": "StarDist_BF_cancer_cell_dataset_20x"
                    },
                    "persistent_identifier": "doi:10.5281/zenodo.10572122",
                    "state": "published",
                    "created": "2025-03-17T05:57:58Z",
                    "version": 1
                }
            ],
            "published_revision": 1,
            "version": 1,
            "api_version": 3,
            "metadata_repository": "Fairdata"
        },
        {
            "id": "e1baf1b8-a843-435d-a3a6-648a1ea4ebbc",
            "access_rights": {
                "id": "b4799718-629c-4c40-a137-2e33f37a889c",
                "license": [
                    {
                        "id": "35b18e72-3819-4ec6-a1be-14624f29d968",
                        "url": "http://uri.suomi.fi/codelist/fairdata/license/code/CC-BY-4.0",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/license",
                        "pref_label": {
                            "en": "Creative Commons Attribution 4.0 International (CC BY 4.0)",
                            "fi": "Creative Commons Nimeä 4.0 Kansainvälinen (CC BY 4.0)"
                        }
                    }
                ],
                "access_type": {
                    "id": "d01ac02c-fc70-4c68-9434-8383cb693ff0",
                    "url": "http://uri.suomi.fi/codelist/fairdata/access_type/code/open",
                    "in_scheme": "http://uri.suomi.fi/codelist/fairdata/access_type",
                    "pref_label": {
                        "en": "Open",
                        "fi": "Avoin"
                    }
                },
                "restriction_grounds": []
            },
            "actors": [
                {
                    "id": "1cd24e24-78b9-4054-baac-a03619aea6ce",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "70dc5833-5352-4320-8017-2c2e83c5a31a",
                        "name": "Gautier Follain"
                    },
                    "organization": {
                        "id": "c876330d-9c3d-4783-9f09-72fbbe2abbf3",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "d98a754d-d545-4715-a2d1-c2b9246be313",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "1ac9a9da-bac7-4b23-a66f-0ef2013f6913",
                        "name": "Sujan Ghimire",
                        "external_identifier": "https://orcid.org/0000-0003-3660-4300"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "137f5d4c-d311-41f6-8f91-83524a0427fb",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "079d8636-4850-43d4-9fdb-fe576c413414",
                        "name": "Joanna Pylvänäinen",
                        "external_identifier": "https://orcid.org/0000-0002-3540-5150"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "94a33002-a672-49a3-b638-5ddf39c2785c",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "7e36e72d-4d24-40a2-a43b-3aa8d900bb0b",
                        "name": "Johanna Ivaska"
                    },
                    "organization": {
                        "id": "c876330d-9c3d-4783-9f09-72fbbe2abbf3",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "e1a28177-9b24-4dae-bec4-4c8110159112",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "4751aa60-4d33-440f-8c1d-15c969e01e5c",
                        "name": "Guillaume Jacquemet",
                        "external_identifier": "https://orcid.org/0000-0002-9286-920X"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "a6fdcab1-5bc5-4a09-8be4-90f844ad8084",
                    "roles": [
                        "publisher"
                    ],
                    "organization": {
                        "id": "9ad0720c-50d0-44f8-8959-13675b17e890",
                        "pref_label": {
                            "en": "Zenodo",
                            "fi": "Zenodo",
                            "sv": "Zenodo"
                        }
                    }
                }
            ],
            "cumulative_state": 0,
            "data_catalog": "urn:nbn:fi:att:data-catalog-abo",
            "description": {
                "en": "This repository includes a StarDist deep learning model and its training and validation datasets for detecting neutrophils perfused over an endothelial cell monolayer. The model was trained on 36 manually annotated images, achieving an average F1 Score of 0.969. The dataset and model are intended for use in biomedical research, particularly for analyzing interactions between neutrophils and endothelial cells. Specifications Model: StarDist for neutrophil detection on endothelial cells Training Dataset: Number of Images: 36 paired brightfield microscopy images and label masks Microscope: Nikon Eclipse Ti2-E, 20x objective Data Type: Brightfield microscopy images with manually segmented masks File Format: TIFF (.tif) Brightfield Images: 16-bit Masks: 8-bit Image Size: 1024 x 1022 pixels (Pixel size: 650 nm) Training Parameters: Epochs: 400 Patch Size: 992 x 992 pixels Batch Size: 2 Performance: Average F1 Score: 0.969 Average IoU: 0.914 Model Training: Conducted using ZeroCostDL4Mic (https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki) Reference Biorxiv paper"
            },
            "field_of_science": [
                {
                    "id": "e9745cdf-d0e1-4797-8fee-3324e5b2bee2",
                    "url": "http://www.yso.fi/onto/okm-tieteenala/ta1182",
                    "in_scheme": "http://www.yso.fi/onto/okm-tieteenala/conceptscheme",
                    "pref_label": {
                        "en": "Biochemistry, cell and molecular biology",
                        "fi": "Biokemia, solu- ja molekyylibiologia",
                        "sv": "Biokemi, cell- och molekylärbiologi"
                    }
                }
            ],
            "infrastructure": [],
            "issued": "2024-01-26",
            "keyword": [
                "neutrophils",
                "Biochemistry and Cell Biology"
            ],
            "language": [],
            "metadata_owner": {
                "id": "dde6b62a-99e9-49c2-92bc-4a08ae3d9a09",
                "organization": "service_abo"
            },
            "other_identifiers": [],
            "persistent_identifier": "doi:10.5281/zenodo.10572231",
            "pid_generated_by_fairdata": false,
            "projects": [],
            "provenance": [],
            "relation": [],
            "remote_resources": [],
            "spatial": [],
            "state": "published",
            "temporal": [],
            "theme": [],
            "title": {
                "en": "StarDist_BF_Neutrophil_dataset"
            },
            "created": "2025-03-17T05:57:56Z",
            "modified": "2025-03-17T05:57:56Z",
            "dataset_versions": [
                {
                    "id": "e1baf1b8-a843-435d-a3a6-648a1ea4ebbc",
                    "title": {
                        "en": "StarDist_BF_Neutrophil_dataset"
                    },
                    "persistent_identifier": "doi:10.5281/zenodo.10572231",
                    "state": "published",
                    "created": "2025-03-17T05:57:56Z",
                    "version": 1
                }
            ],
            "published_revision": 1,
            "version": 1,
            "api_version": 3,
            "metadata_repository": "Fairdata"
        },
        {
            "id": "07a0d56e-dab9-4067-9104-eb9155e870f3",
            "access_rights": {
                "id": "2ad6a61e-7d0b-4404-9b30-37bf2b63eaaa",
                "license": [
                    {
                        "id": "35b18e72-3819-4ec6-a1be-14624f29d968",
                        "url": "http://uri.suomi.fi/codelist/fairdata/license/code/CC-BY-4.0",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/license",
                        "pref_label": {
                            "en": "Creative Commons Attribution 4.0 International (CC BY 4.0)",
                            "fi": "Creative Commons Nimeä 4.0 Kansainvälinen (CC BY 4.0)"
                        }
                    }
                ],
                "access_type": {
                    "id": "d01ac02c-fc70-4c68-9434-8383cb693ff0",
                    "url": "http://uri.suomi.fi/codelist/fairdata/access_type/code/open",
                    "in_scheme": "http://uri.suomi.fi/codelist/fairdata/access_type",
                    "pref_label": {
                        "en": "Open",
                        "fi": "Avoin"
                    }
                },
                "restriction_grounds": []
            },
            "actors": [
                {
                    "id": "0224828d-0d6a-4c7c-ac28-000d5718538e",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "7276b7be-070b-44b7-af15-ec72e8cd87ad",
                        "name": "Gautier Follain"
                    },
                    "organization": {
                        "id": "4ac5eb12-46d4-4aab-9980-0dc8dfc06088",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "3a8d84fc-ad65-43d8-9140-52de77f0c88d",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "900dcf89-9c78-4675-ab0a-b6e934aa04db",
                        "name": "Sujan Ghimire",
                        "external_identifier": "https://orcid.org/0000-0003-3660-4300"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "914d5290-7fed-4309-84c3-562b0eea64c1",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "235f6872-180b-48ac-98cc-05db7b0a3a58",
                        "name": "Joanna Pylvänäinen",
                        "external_identifier": "https://orcid.org/0000-0002-3540-5150"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "19060b77-bc2e-4743-bd1b-5e9bf4567df9",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "38a104ea-4272-48c1-ad82-c8ddf7ff8863",
                        "name": "Johanna Ivaska"
                    },
                    "organization": {
                        "id": "4ac5eb12-46d4-4aab-9980-0dc8dfc06088",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "72ff6e9a-a3d7-42a8-9a3c-68137ca93ce5",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "4c597145-e8ee-48bc-a3dc-b7316059bac1",
                        "name": "Guillaume Jacquemet",
                        "external_identifier": "https://orcid.org/0000-0002-9286-920X"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "f78d5442-59b9-47b9-bc88-1b79e99af4b0",
                    "roles": [
                        "publisher"
                    ],
                    "organization": {
                        "id": "6946b9c2-c9fe-4c40-a840-d42334ebd20d",
                        "pref_label": {
                            "en": "Zenodo",
                            "fi": "Zenodo",
                            "sv": "Zenodo"
                        }
                    }
                }
            ],
            "cumulative_state": 0,
            "data_catalog": "urn:nbn:fi:att:data-catalog-abo",
            "description": {
                "en": "This repository includes a StarDist deep learning model and its training and validation datasets for detecting fluorescently labeled cancer cells perfused over an endothelial cell monolayer. The model was trained on 66 images labeled with CellTrace and demonstrated high accuracy, achieving an average F1 Score of 0.877. The dataset and the trained model can be used for biomedical image analysis, particularly in cancer research. Specifications Model: StarDist for cancer cell detection Training Dataset: Number of Images: 66 paired fluorescent microscopy images and label masks Microscope: Nikon Eclipse Ti2-E, 10x objective Data Type: Fluorescent microscopy images with manually segmented masks File Format: TIFF (.tif) Brightfield Images: 16-bit Masks: 8-bit Image Size: 1024 x 1024 pixels (Pixel size: 1.3205 μm) Training Parameters: Epochs: 200 Patch Size: 1024 x 1024 pixels Batch Size: 2 Performance: Average F1 Score: 0.877 Average IoU: 0.646 Model Training: Conducted using ZeroCostDL4Mic (https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki) Reference Biorxiv paper"
            },
            "field_of_science": [
                {
                    "id": "e9745cdf-d0e1-4797-8fee-3324e5b2bee2",
                    "url": "http://www.yso.fi/onto/okm-tieteenala/ta1182",
                    "in_scheme": "http://www.yso.fi/onto/okm-tieteenala/conceptscheme",
                    "pref_label": {
                        "en": "Biochemistry, cell and molecular biology",
                        "fi": "Biokemia, solu- ja molekyylibiologia",
                        "sv": "Biokemi, cell- och molekylärbiologi"
                    }
                }
            ],
            "infrastructure": [],
            "issued": "2024-01-26",
            "keyword": [
                "Biochemistry and Cell Biology"
            ],
            "language": [],
            "metadata_owner": {
                "id": "dde6b62a-99e9-49c2-92bc-4a08ae3d9a09",
                "organization": "service_abo"
            },
            "other_identifiers": [],
            "persistent_identifier": "doi:10.5281/zenodo.10572310",
            "pid_generated_by_fairdata": false,
            "projects": [],
            "provenance": [],
            "relation": [],
            "remote_resources": [],
            "spatial": [],
            "state": "published",
            "temporal": [],
            "theme": [],
            "title": {
                "en": "StarDist_Fluorescent_cells"
            },
            "created": "2025-03-17T05:57:54Z",
            "modified": "2025-03-17T05:57:54Z",
            "dataset_versions": [
                {
                    "id": "07a0d56e-dab9-4067-9104-eb9155e870f3",
                    "title": {
                        "en": "StarDist_Fluorescent_cells"
                    },
                    "persistent_identifier": "doi:10.5281/zenodo.10572310",
                    "state": "published",
                    "created": "2025-03-17T05:57:54Z",
                    "version": 1
                }
            ],
            "published_revision": 1,
            "version": 1,
            "api_version": 3,
            "metadata_repository": "Fairdata"
        },
        {
            "id": "28fcd5d4-6749-41a6-bd84-1b11df7755da",
            "access_rights": {
                "id": "0c14452a-ce9f-497d-90de-ce5791e46465",
                "license": [
                    {
                        "id": "35b18e72-3819-4ec6-a1be-14624f29d968",
                        "url": "http://uri.suomi.fi/codelist/fairdata/license/code/CC-BY-4.0",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/license",
                        "pref_label": {
                            "en": "Creative Commons Attribution 4.0 International (CC BY 4.0)",
                            "fi": "Creative Commons Nimeä 4.0 Kansainvälinen (CC BY 4.0)"
                        }
                    }
                ],
                "access_type": {
                    "id": "d01ac02c-fc70-4c68-9434-8383cb693ff0",
                    "url": "http://uri.suomi.fi/codelist/fairdata/access_type/code/open",
                    "in_scheme": "http://uri.suomi.fi/codelist/fairdata/access_type",
                    "pref_label": {
                        "en": "Open",
                        "fi": "Avoin"
                    }
                },
                "restriction_grounds": []
            },
            "actors": [
                {
                    "id": "dcec39da-8496-4cb3-8908-5b1cafafca3b",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "d6a40115-3024-46da-8f6f-eaea08c210a8",
                        "name": "Gautier Follain"
                    },
                    "organization": {
                        "id": "2b780346-72d9-4e30-895b-6bb2d7cf3fdf",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "a396d7f2-1420-4be1-91d9-57eb5a8bc5da",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "d454229d-ebc5-41ab-b500-f6262eea7a7c",
                        "name": "Sujan Ghimire",
                        "external_identifier": "https://orcid.org/0000-0003-3660-4300"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "8d05db2a-32c3-46a1-a121-803848b08489",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "80c7d0f8-ec01-43be-84ce-2166452dc256",
                        "name": "Joanna Pylvänäinen",
                        "external_identifier": "https://orcid.org/0000-0002-3540-5150"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "0756ddf0-1507-4c73-a0e1-fafa3ee05007",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "10b9c567-500e-41af-b079-9b59f40967f3",
                        "name": "Johanna Ivaska"
                    },
                    "organization": {
                        "id": "2b780346-72d9-4e30-895b-6bb2d7cf3fdf",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "2a2ac05f-d8b8-46df-9b90-c7db03674125",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "4583efbc-705a-44f8-9ce7-5598ae0f203b",
                        "name": "Guillaume Jacquemet",
                        "external_identifier": "https://orcid.org/0000-0002-9286-920X"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "9cd19088-6758-4b11-b3b6-bb360f696cc5",
                    "roles": [
                        "publisher"
                    ],
                    "organization": {
                        "id": "6d91a78d-b8f0-4d2d-93b0-83f5f5035118",
                        "pref_label": {
                            "en": "Zenodo",
                            "fi": "Zenodo",
                            "sv": "Zenodo"
                        }
                    }
                }
            ],
            "cumulative_state": 0,
            "data_catalog": "urn:nbn:fi:att:data-catalog-abo",
            "description": {
                "en": "This repository includes a StarDist deep learning model and its training and validation datasets for detecting mononucleated cells perfused over an endothelial cell monolayer. The model was trained on 27 manually annotated images and achieved an average F1 Score of 0.941. The dataset and model are helpful for biomedical research, especially in studying interactions between mononucleated and endothelial cells. Specifications Model: StarDist for mononucleated cell detection on endothelial cells Training Dataset: Number of Images: 27 paired brightfield microscopy images and label masks Microscope: Nikon Eclipse Ti2-E, 20x objective Data Type: Brightfield microscopy images with manually segmented masks File Format: TIFF (.tif) Brightfield Images: 16-bit Masks: 8-bit Image Size: 1024 x 1022 pixels (Pixel size: 650 nm) Training Parameters: Epochs: 400 Patch Size: 992 x 992 pixels Batch Size: 2 Performance: Average F1 Score: 0.941 Average IoU: 0.831 Model Training: Conducted using ZeroCostDL4Mic (https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki) Reference Biorxiv paper"
            },
            "field_of_science": [
                {
                    "id": "e9745cdf-d0e1-4797-8fee-3324e5b2bee2",
                    "url": "http://www.yso.fi/onto/okm-tieteenala/ta1182",
                    "in_scheme": "http://www.yso.fi/onto/okm-tieteenala/conceptscheme",
                    "pref_label": {
                        "en": "Biochemistry, cell and molecular biology",
                        "fi": "Biokemia, solu- ja molekyylibiologia",
                        "sv": "Biokemi, cell- och molekylärbiologi"
                    }
                }
            ],
            "infrastructure": [],
            "issued": "2024-01-26",
            "keyword": [
                "Biochemistry and Cell Biology"
            ],
            "language": [],
            "metadata_owner": {
                "id": "dde6b62a-99e9-49c2-92bc-4a08ae3d9a09",
                "organization": "service_abo"
            },
            "other_identifiers": [],
            "persistent_identifier": "doi:10.5281/zenodo.10572200",
            "pid_generated_by_fairdata": false,
            "projects": [],
            "provenance": [],
            "relation": [],
            "remote_resources": [],
            "spatial": [],
            "state": "published",
            "temporal": [],
            "theme": [],
            "title": {
                "en": "StarDist_BF_Monocytes_dataset"
            },
            "created": "2025-03-17T05:57:52Z",
            "modified": "2025-03-17T05:57:52Z",
            "dataset_versions": [
                {
                    "id": "28fcd5d4-6749-41a6-bd84-1b11df7755da",
                    "title": {
                        "en": "StarDist_BF_Monocytes_dataset"
                    },
                    "persistent_identifier": "doi:10.5281/zenodo.10572200",
                    "state": "published",
                    "created": "2025-03-17T05:57:52Z",
                    "version": 1
                }
            ],
            "published_revision": 1,
            "version": 1,
            "api_version": 3,
            "metadata_repository": "Fairdata"
        },
        {
            "id": "004ea44c-0561-4c6c-8706-41728a0429d1",
            "access_rights": {
                "id": "312f9aa1-4d9b-41e4-97db-e82d6be12e91",
                "license": [
                    {
                        "id": "6142d0c6-945d-4085-b9f7-81e52afa253b",
                        "url": "http://uri.suomi.fi/codelist/fairdata/license/code/other",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/license",
                        "pref_label": {
                            "en": "Other",
                            "fi": "Muu"
                        }
                    }
                ],
                "access_type": {
                    "id": "d01ac02c-fc70-4c68-9434-8383cb693ff0",
                    "url": "http://uri.suomi.fi/codelist/fairdata/access_type/code/open",
                    "in_scheme": "http://uri.suomi.fi/codelist/fairdata/access_type",
                    "pref_label": {
                        "en": "Open",
                        "fi": "Avoin"
                    }
                },
                "restriction_grounds": []
            },
            "actors": [
                {
                    "id": "19c8f8bf-bae1-4fe5-9591-500bc763b516",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "2618daa8-7a55-4d7c-b56b-207536d8d6f9",
                        "name": "Gautier Follain"
                    },
                    "organization": {
                        "id": "2c8a8f66-5d67-4fd8-8ecb-948294c68bca",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "c81b510e-0220-4818-b7d5-664eec9d2d16",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "fe9339f1-2c4e-4616-b540-434936e25c01",
                        "name": "Sujan Ghimire",
                        "external_identifier": "https://orcid.org/0000-0003-3660-4300"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "40faf64f-c429-4251-996f-2ad617d7a801",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "1d57cccd-96e4-4927-abde-0eaa8cc947f8",
                        "name": "Joanna Pylvänäinen",
                        "external_identifier": "https://orcid.org/0000-0002-3540-5150"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "72b6864f-f105-4571-9123-16c52b0b3818",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "18b84fe8-c844-4a32-8bf5-aeb21a123075",
                        "name": "Johanna Ivaska"
                    },
                    "organization": {
                        "id": "2c8a8f66-5d67-4fd8-8ecb-948294c68bca",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "2af2f2fb-e143-40ab-be95-e66d69bc9ffb",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "4818c445-4f03-4609-a5b7-47fb8907bbaa",
                        "name": "Guillaume Jacquemet",
                        "external_identifier": "https://orcid.org/0000-0002-9286-920X"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "6326973b-4a25-46a8-91f6-c349e45fd891",
                    "roles": [
                        "publisher"
                    ],
                    "organization": {
                        "id": "44f7f447-cddd-4bfe-b73d-1e9f42f75b04",
                        "pref_label": {
                            "en": "Zenodo",
                            "fi": "Zenodo",
                            "sv": "Zenodo"
                        }
                    }
                }
            ],
            "cumulative_state": 0,
            "data_catalog": "urn:nbn:fi:att:data-catalog-abo",
            "description": {
                "en": "This repository contains a Pix2Pix deep learning model to generate synthetic PECAM-1 staining from brightfield images. The model was trained on an initial dataset of 484 paired brightfield and fluorescent microscopy images, which was computationally augmented by a factor of 6 to enhance model performance. The training was conducted over 245 epochs with a patch size of 512x512, a batch size of 1, and a vanilla GAN loss function. The final model was selected based on quality metric scores and visual comparison to ground truth images, achieving an average SSIM score of 0.273 and an LPIPS score of 0.360 on the test dataset. Specifications Model: Pix2Pix for generating synthetic PECAM staining from brightfield images Training Dataset: Original Dataset: 484 paired brightfield and fluorescent microscopy images Augmented Dataset: Expanded to 2,904 paired images through computational augmentation Microscope: Nikon Eclipse Ti2-E, brightfield/fluorescence microscope with a 20x objective Data Type: Brightfield and fluorescent microscopy images File Format: TIFF (.tif), 16-bit Image Size: 1024 x 1022 pixels (Pixel size: 650 nm) Training Parameters: Epochs: 245 Patch Size: 512 x 512 pixels Batch Size: 1 Loss Function: Vanilla GAN loss function Model Performance: SSIM Score: 0.273 LPIPS Score: 0.360 Model Selection: The best model was chosen based on quality metric scores and visual inspection compared to ground truth images. Model Training: Conducted using ZeroCostDL4Mic (https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki) Reference Biorxiv paper"
            },
            "field_of_science": [
                {
                    "id": "e9745cdf-d0e1-4797-8fee-3324e5b2bee2",
                    "url": "http://www.yso.fi/onto/okm-tieteenala/ta1182",
                    "in_scheme": "http://www.yso.fi/onto/okm-tieteenala/conceptscheme",
                    "pref_label": {
                        "en": "Biochemistry, cell and molecular biology",
                        "fi": "Biokemia, solu- ja molekyylibiologia",
                        "sv": "Biokemi, cell- och molekylärbiologi"
                    }
                }
            ],
            "infrastructure": [],
            "issued": "2024-02-02",
            "keyword": [
                "Biochemistry and Cell Biology"
            ],
            "language": [],
            "metadata_owner": {
                "id": "dde6b62a-99e9-49c2-92bc-4a08ae3d9a09",
                "organization": "service_abo"
            },
            "other_identifiers": [],
            "persistent_identifier": "doi:10.5281/zenodo.10611092",
            "pid_generated_by_fairdata": false,
            "projects": [],
            "provenance": [],
            "relation": [],
            "remote_resources": [],
            "spatial": [],
            "state": "published",
            "temporal": [],
            "theme": [],
            "title": {
                "en": "pix2pix_HUVEC_juctions_dataset"
            },
            "created": "2025-03-17T05:57:49Z",
            "modified": "2025-03-17T05:57:49Z",
            "dataset_versions": [
                {
                    "id": "004ea44c-0561-4c6c-8706-41728a0429d1",
                    "title": {
                        "en": "pix2pix_HUVEC_juctions_dataset"
                    },
                    "persistent_identifier": "doi:10.5281/zenodo.10611092",
                    "state": "published",
                    "created": "2025-03-17T05:57:49Z",
                    "version": 1
                }
            ],
            "published_revision": 1,
            "version": 1,
            "api_version": 3,
            "metadata_repository": "Fairdata"
        },
        {
            "id": "3ab84a7f-7b39-4891-a1e0-f638c150c72b",
            "access_rights": {
                "id": "f6d4a8b5-278d-42e2-907d-ecea3f79f7b4",
                "license": [
                    {
                        "id": "35b18e72-3819-4ec6-a1be-14624f29d968",
                        "url": "http://uri.suomi.fi/codelist/fairdata/license/code/CC-BY-4.0",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/license",
                        "pref_label": {
                            "en": "Creative Commons Attribution 4.0 International (CC BY 4.0)",
                            "fi": "Creative Commons Nimeä 4.0 Kansainvälinen (CC BY 4.0)"
                        }
                    }
                ],
                "access_type": {
                    "id": "d01ac02c-fc70-4c68-9434-8383cb693ff0",
                    "url": "http://uri.suomi.fi/codelist/fairdata/access_type/code/open",
                    "in_scheme": "http://uri.suomi.fi/codelist/fairdata/access_type",
                    "pref_label": {
                        "en": "Open",
                        "fi": "Avoin"
                    }
                },
                "restriction_grounds": []
            },
            "actors": [
                {
                    "id": "62b2f4a5-49cd-4cd4-8dfe-3c9415ad327c",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "b54f3b5f-a0f6-4cc0-8ce5-ba2bff891734",
                        "name": "Gautier Follain"
                    },
                    "organization": {
                        "id": "6feb752f-13e4-4813-b686-34cf7f4336ff",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "c4223bb6-5fb5-4156-bfe2-8f62ebedfa59",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "f313e0e4-da19-4858-ad86-5b0f53e49650",
                        "name": "Sujan Ghimire",
                        "external_identifier": "https://orcid.org/0000-0003-3660-4300"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "36867839-6d40-467f-b376-467eb4577368",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "58623938-e317-4c2a-a18d-faf55b110f32",
                        "name": "Joanna Pylvänäinen",
                        "external_identifier": "https://orcid.org/0000-0002-3540-5150"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "17006a66-c57f-41be-b7c5-775a15586855",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "f294ae83-6a77-41f7-9ae7-b3449d4dde43",
                        "name": "Johanna Ivaska"
                    },
                    "organization": {
                        "id": "6feb752f-13e4-4813-b686-34cf7f4336ff",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "15a98c38-0332-4405-93f9-65d197c4ac01",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "7790dff0-af72-4db7-a215-8ec07ece186e",
                        "name": "Guillaume Jacquemet",
                        "external_identifier": "https://orcid.org/0000-0002-9286-920X"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "29cba276-36be-4619-8868-001a1e7558cb",
                    "roles": [
                        "publisher"
                    ],
                    "organization": {
                        "id": "095374fc-c177-42d2-9a46-3b769cacd004",
                        "pref_label": {
                            "en": "Zenodo",
                            "fi": "Zenodo",
                            "sv": "Zenodo"
                        }
                    }
                }
            ],
            "cumulative_state": 0,
            "data_catalog": "urn:nbn:fi:att:data-catalog-abo",
            "description": {
                "en": "This repository contains a Pix2Pix deep learning model to generate synthetic nuclear staining from brightfield images. The model was trained on 258 paired brightfield and fluorescent microscopy images of circulating cancer cells perfused over an endothelial cell monolayer. To improve performance, the dataset was augmented computationally by a factor of 8. The model was trained over 400 epochs using a patch size of 512x512, a batch size of 1, and a vanilla GAN loss function. The final model was selected based on its performance metrics and visual fidelity when compared to ground truth images, achieving an average SSIM score of 0.755 and an LPIPS score of 0.120. Specifications Model: Pix2Pix for generating synthetic nuclear staining from brightfield images Training Dataset: Cancer Cells: 258 paired brightfield and fluorescent microscopy images Microscope: Nikon Eclipse Ti2-E, brightfield/fluorescence microscope with a 20x objective Data Type: Brightfield and fluorescent microscopy images File Format: TIFF (.tif), 16-bit Image Size: 1024 x 1022 pixels (Pixel size: 650 nm) Training Parameters: Epochs: 400 Patch Size: 512 x 512 pixels Batch Size: 1 Loss Function: Vanilla GAN loss function Model Performance: Circulating Cancer Cells: SSIM Score: 0.755 LPIPS Score: 0.120 Model Selection: Models were selected based on quality metric scores and visual inspection compared to ground truth images. Model Training: Conducted using ZeroCostDL4Mic (https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki) Reference Biorxiv paper"
            },
            "field_of_science": [
                {
                    "id": "e9745cdf-d0e1-4797-8fee-3324e5b2bee2",
                    "url": "http://www.yso.fi/onto/okm-tieteenala/ta1182",
                    "in_scheme": "http://www.yso.fi/onto/okm-tieteenala/conceptscheme",
                    "pref_label": {
                        "en": "Biochemistry, cell and molecular biology",
                        "fi": "Biokemia, solu- ja molekyylibiologia",
                        "sv": "Biokemi, cell- och molekylärbiologi"
                    }
                }
            ],
            "infrastructure": [],
            "issued": "2024-02-05",
            "keyword": [
                "Biochemistry and Cell Biology"
            ],
            "language": [],
            "metadata_owner": {
                "id": "dde6b62a-99e9-49c2-92bc-4a08ae3d9a09",
                "organization": "service_abo"
            },
            "other_identifiers": [],
            "persistent_identifier": "doi:10.5281/zenodo.10621667",
            "pid_generated_by_fairdata": false,
            "projects": [],
            "provenance": [],
            "relation": [],
            "remote_resources": [],
            "spatial": [],
            "state": "published",
            "temporal": [],
            "theme": [],
            "title": {
                "en": "pix2pix_HUVEC_nuclei_cancer_cells_dataset"
            },
            "created": "2025-03-17T05:57:47Z",
            "modified": "2025-03-17T05:57:47Z",
            "dataset_versions": [
                {
                    "id": "3ab84a7f-7b39-4891-a1e0-f638c150c72b",
                    "title": {
                        "en": "pix2pix_HUVEC_nuclei_cancer_cells_dataset"
                    },
                    "persistent_identifier": "doi:10.5281/zenodo.10621667",
                    "state": "published",
                    "created": "2025-03-17T05:57:47Z",
                    "version": 1
                }
            ],
            "published_revision": 1,
            "version": 1,
            "api_version": 3,
            "metadata_repository": "Fairdata"
        },
        {
            "id": "e1043cae-a46e-40a9-b051-878da9423b39",
            "access_rights": {
                "id": "69234734-e49e-4f60-94ef-c501d910b443",
                "license": [
                    {
                        "id": "35b18e72-3819-4ec6-a1be-14624f29d968",
                        "url": "http://uri.suomi.fi/codelist/fairdata/license/code/CC-BY-4.0",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/license",
                        "pref_label": {
                            "en": "Creative Commons Attribution 4.0 International (CC BY 4.0)",
                            "fi": "Creative Commons Nimeä 4.0 Kansainvälinen (CC BY 4.0)"
                        }
                    }
                ],
                "access_type": {
                    "id": "d01ac02c-fc70-4c68-9434-8383cb693ff0",
                    "url": "http://uri.suomi.fi/codelist/fairdata/access_type/code/open",
                    "in_scheme": "http://uri.suomi.fi/codelist/fairdata/access_type",
                    "pref_label": {
                        "en": "Open",
                        "fi": "Avoin"
                    }
                },
                "restriction_grounds": []
            },
            "actors": [
                {
                    "id": "6bba3b3c-42be-4652-baa9-a30e4516e7d0",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "e9b04076-57c3-4b6a-bc34-4291f3926204",
                        "name": "Gautier Follain"
                    },
                    "organization": {
                        "id": "82cdedd1-686e-4f90-b041-3adc44d41ec1",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "f2507ddd-b86b-4ec3-8c8a-879c70c4994c",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "206cae5b-055f-48f9-a607-3cca76b618bb",
                        "name": "Sujan Ghimire",
                        "external_identifier": "https://orcid.org/0000-0003-3660-4300"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "ba27d902-d4eb-47fe-ab25-fe1322ffd184",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "bf373314-0634-45d9-a171-0f6206b47281",
                        "name": "Joanna Pylvänäinen",
                        "external_identifier": "https://orcid.org/0000-0002-3540-5150"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "52466003-9cae-4d12-a614-6e9621ac724b",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "7a1f1b63-dd90-4098-bfb7-c14df28ee3d2",
                        "name": "Johanna Ivaska"
                    },
                    "organization": {
                        "id": "82cdedd1-686e-4f90-b041-3adc44d41ec1",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "1d6a28a3-cd4e-42d8-a68e-d5a81d52718a",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "20b3d321-86a6-4154-8ed6-7de8bcd1c1cc",
                        "name": "Guillaume Jacquemet",
                        "external_identifier": "https://orcid.org/0000-0002-9286-920X"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "5a24b3fa-f5a0-400c-8e5e-7d80f6d66f22",
                    "roles": [
                        "publisher"
                    ],
                    "organization": {
                        "id": "6c20169f-d9db-4170-8690-53a38724bbaf",
                        "pref_label": {
                            "en": "Zenodo",
                            "fi": "Zenodo",
                            "sv": "Zenodo"
                        }
                    }
                }
            ],
            "cumulative_state": 0,
            "data_catalog": "urn:nbn:fi:att:data-catalog-abo",
            "description": {
                "en": "This repository contains a Pix2Pix deep learning model designed to generate synthetic nuclear staining from brightfield images of circulating immune cells. The model was trained on a dataset of 226 paired brightfield and fluorescent microscopy images, which were augmented computationally by a factor of 8 to enhance model performance. The model was trained over 400 epochs using a patch size of 512x512, a batch size of 1, and a vanilla GAN loss function. The final model was selected based on quality metric scores and visual comparison to ground truth images, achieving an average SSIM score of 0.756 and an LPIPS score of 0.130. Specifications Model: Pix2Pix for generating synthetic nuclear staining from brightfield images of circulating immune cells Training Dataset: Immune Cells: 226 paired brightfield and fluorescent microscopy images Microscope: Nikon Eclipse Ti2-E, brightfield/fluorescence microscope with a 20x objective Data Type: Brightfield and fluorescent microscopy images File Format: TIFF (.tif), 16-bit Image Size: 1024 x 1022 pixels (Pixel size: 650 nm) Training Parameters: Epochs: 400 Patch Size: 512 x 512 pixels Batch Size: 1 Loss Function: Vanilla GAN loss function Model Performance: Immune Cells: SSIM Score: 0.756 LPIPS Score: 0.130 Model Selection: Models were chosen based on quality metric scores and visual inspection compared to ground truth images. Model Training: Conducted using ZeroCostDL4Mic (https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki) Reference Biorxiv paper"
            },
            "field_of_science": [
                {
                    "id": "e9745cdf-d0e1-4797-8fee-3324e5b2bee2",
                    "url": "http://www.yso.fi/onto/okm-tieteenala/ta1182",
                    "in_scheme": "http://www.yso.fi/onto/okm-tieteenala/conceptscheme",
                    "pref_label": {
                        "en": "Biochemistry, cell and molecular biology",
                        "fi": "Biokemia, solu- ja molekyylibiologia",
                        "sv": "Biokemi, cell- och molekylärbiologi"
                    }
                }
            ],
            "infrastructure": [],
            "issued": "2024-02-05",
            "keyword": [
                "Biochemistry and Cell Biology"
            ],
            "language": [],
            "metadata_owner": {
                "id": "dde6b62a-99e9-49c2-92bc-4a08ae3d9a09",
                "organization": "service_abo"
            },
            "other_identifiers": [],
            "persistent_identifier": "doi:10.5281/zenodo.10617565",
            "pid_generated_by_fairdata": false,
            "projects": [],
            "provenance": [],
            "relation": [],
            "remote_resources": [],
            "spatial": [],
            "state": "published",
            "temporal": [],
            "theme": [],
            "title": {
                "en": "pix2pix_HUVEC_nuclei_immuno_cells_dataset"
            },
            "created": "2025-03-17T05:57:45Z",
            "modified": "2025-03-17T05:57:45Z",
            "dataset_versions": [
                {
                    "id": "e1043cae-a46e-40a9-b051-878da9423b39",
                    "title": {
                        "en": "pix2pix_HUVEC_nuclei_immuno_cells_dataset"
                    },
                    "persistent_identifier": "doi:10.5281/zenodo.10617565",
                    "state": "published",
                    "created": "2025-03-17T05:57:45Z",
                    "version": 1
                }
            ],
            "published_revision": 1,
            "version": 1,
            "api_version": 3,
            "metadata_repository": "Fairdata"
        },
        {
            "id": "f53395f6-6c1d-4fcc-8d3a-fefce3befb6f",
            "access_rights": {
                "id": "b07f1433-e252-4438-9d49-edb3e336b98d",
                "license": [
                    {
                        "id": "35b18e72-3819-4ec6-a1be-14624f29d968",
                        "url": "http://uri.suomi.fi/codelist/fairdata/license/code/CC-BY-4.0",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/license",
                        "pref_label": {
                            "en": "Creative Commons Attribution 4.0 International (CC BY 4.0)",
                            "fi": "Creative Commons Nimeä 4.0 Kansainvälinen (CC BY 4.0)"
                        }
                    }
                ],
                "access_type": {
                    "id": "d01ac02c-fc70-4c68-9434-8383cb693ff0",
                    "url": "http://uri.suomi.fi/codelist/fairdata/access_type/code/open",
                    "in_scheme": "http://uri.suomi.fi/codelist/fairdata/access_type",
                    "pref_label": {
                        "en": "Open",
                        "fi": "Avoin"
                    }
                },
                "restriction_grounds": []
            },
            "actors": [
                {
                    "id": "c219a0d5-6a63-49e0-8586-3ae70e8f7ab5",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "7f6f0cf5-f201-4dd5-953a-6d8fd309da71",
                        "name": "Gautier Follain"
                    },
                    "organization": {
                        "id": "27f5beb3-32de-4a15-851c-3769a1077e63",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "cd42c100-da6d-4df5-b9f6-b9b6ef5aad67",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "a780de1a-a1cb-4445-84b0-91a70e2f967e",
                        "name": "Sujan Ghimire",
                        "external_identifier": "https://orcid.org/0000-0003-3660-4300"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "49dc174d-28cd-405b-853a-dec6834ce518",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "1b4fbb48-e866-4d98-8c18-b1884a8f51b8",
                        "name": "Joanna Pylvänäinen",
                        "external_identifier": "https://orcid.org/0000-0002-3540-5150"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "ee1e85e6-c02f-4e28-b358-dc1ad98032c9",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "63a1b880-6561-43f2-9042-8dabb3dab4f5",
                        "name": "Johanna Ivaska"
                    },
                    "organization": {
                        "id": "27f5beb3-32de-4a15-851c-3769a1077e63",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "cb2259dd-70da-4f97-9198-a7ef07595f86",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "55f54914-83c7-4e57-8d55-e15a232a69d3",
                        "name": "Guillaume Jacquemet",
                        "external_identifier": "https://orcid.org/0000-0002-9286-920X"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "3caef57e-9340-401a-8f16-3479d3adb02e",
                    "roles": [
                        "publisher"
                    ],
                    "organization": {
                        "id": "ee3a2560-d64e-4775-85c7-b57a34a4a91f",
                        "pref_label": {
                            "en": "Zenodo",
                            "fi": "Zenodo",
                            "sv": "Zenodo"
                        }
                    }
                }
            ],
            "cumulative_state": 0,
            "data_catalog": "urn:nbn:fi:att:data-catalog-abo",
            "description": {
                "en": "This repository contains a StarDist deep learning model and its training and validation datasets for segmenting endothelial nuclei while ignoring cancer cells. The cancer cells were perfused over an endothelial cell monolayer. The initial dataset consisted of 17 images, where cancer cell nuclei were manually removed after segmentation with the StarDist Versatile Nuclei model. This dataset was augmented to 68 paired images using computational techniques like rotation and flipping. The model was trained for 200 epochs, achieving an average F1 Score of 0.976, demonstrating high accuracy in segmenting endothelial nuclei while excluding cancer cells. Specifications Model: StarDist for segmenting endothelial nuclei while ignoring cancer cells Training Dataset: Number of Original Images: 17 paired predictions of nuclei and label images Augmented Dataset: Expanded to 68 paired images using rotation and flipping Source Image Generation: Generated using a pix2pix model trained to predict nuclei from brightfield images of cancer cells on top of an endothelium (DOI: 10.5281/zenodo.10617532) Target Image Generation: Masks obtained via manual segmentation File Format: TIFF (.tif) Brightfield Images: 8-bit Masks: 8-bit Image Size: 1024 x 1022 pixels (uncalibrated) Training Parameters: Epochs: 200 Patch Size: 1024 x 1024 pixels Batch Size: 2 Performance: Average F1 Score: 0.976 Average IoU: 0.927 Model Training: Conducted using ZeroCostDL4Mic (https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki) Reference Biorxiv paper"
            },
            "field_of_science": [
                {
                    "id": "e9745cdf-d0e1-4797-8fee-3324e5b2bee2",
                    "url": "http://www.yso.fi/onto/okm-tieteenala/ta1182",
                    "in_scheme": "http://www.yso.fi/onto/okm-tieteenala/conceptscheme",
                    "pref_label": {
                        "en": "Biochemistry, cell and molecular biology",
                        "fi": "Biokemia, solu- ja molekyylibiologia",
                        "sv": "Biokemi, cell- och molekylärbiologi"
                    }
                }
            ],
            "infrastructure": [],
            "issued": "2024-02-05",
            "keyword": [
                "Biochemistry and Cell Biology"
            ],
            "language": [],
            "metadata_owner": {
                "id": "dde6b62a-99e9-49c2-92bc-4a08ae3d9a09",
                "organization": "service_abo"
            },
            "other_identifiers": [],
            "persistent_identifier": "doi:10.5281/zenodo.10617532",
            "pid_generated_by_fairdata": false,
            "projects": [],
            "provenance": [],
            "relation": [],
            "remote_resources": [],
            "spatial": [],
            "state": "published",
            "temporal": [],
            "theme": [],
            "title": {
                "en": "StarDist_HUVEC_nuclei_dataset"
            },
            "created": "2025-03-17T05:57:43Z",
            "modified": "2025-03-17T05:57:43Z",
            "dataset_versions": [
                {
                    "id": "f53395f6-6c1d-4fcc-8d3a-fefce3befb6f",
                    "title": {
                        "en": "StarDist_HUVEC_nuclei_dataset"
                    },
                    "persistent_identifier": "doi:10.5281/zenodo.10617532",
                    "state": "published",
                    "created": "2025-03-17T05:57:43Z",
                    "version": 1
                }
            ],
            "published_revision": 1,
            "version": 1,
            "api_version": 3,
            "metadata_repository": "Fairdata"
        },
        {
            "id": "9b61bdf0-2e18-46e8-827c-2813d79ca91d",
            "access_rights": {
                "id": "6b1e71a6-535d-455f-8591-e0b13b71491f",
                "license": [
                    {
                        "id": "35b18e72-3819-4ec6-a1be-14624f29d968",
                        "url": "http://uri.suomi.fi/codelist/fairdata/license/code/CC-BY-4.0",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/license",
                        "pref_label": {
                            "en": "Creative Commons Attribution 4.0 International (CC BY 4.0)",
                            "fi": "Creative Commons Nimeä 4.0 Kansainvälinen (CC BY 4.0)"
                        }
                    }
                ],
                "access_type": {
                    "id": "d01ac02c-fc70-4c68-9434-8383cb693ff0",
                    "url": "http://uri.suomi.fi/codelist/fairdata/access_type/code/open",
                    "in_scheme": "http://uri.suomi.fi/codelist/fairdata/access_type",
                    "pref_label": {
                        "en": "Open",
                        "fi": "Avoin"
                    }
                },
                "restriction_grounds": []
            },
            "actors": [
                {
                    "id": "bcdf2598-a397-49a8-944d-d259299e557f",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "2375adfd-ecc7-4762-bb9e-22b7ffbda815",
                        "name": "Gautier Follain"
                    },
                    "organization": {
                        "id": "b7c2b304-412b-46b8-9a12-6e0fdc62c172",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "40c9aab6-2efc-48ed-b310-31b8332822d0",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "926ad970-c1a7-4d6e-834d-27b7a5c2b6f8",
                        "name": "Sujan Ghimire",
                        "external_identifier": "https://orcid.org/0000-0003-3660-4300"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "d0e373ef-87ff-442d-9ca1-e2bc92801906",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "27d0cd1a-d6da-4790-9ddc-9276219e2e8a",
                        "name": "Joanna Pylvänäinen",
                        "external_identifier": "https://orcid.org/0000-0002-3540-5150"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "98ed5833-809d-42ba-a214-2f6d384aa56d",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "512a2ca6-5059-428a-8b7d-f4bce9eb87dd",
                        "name": "Johanna Ivaska"
                    },
                    "organization": {
                        "id": "b7c2b304-412b-46b8-9a12-6e0fdc62c172",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "4f741d35-918f-4582-8506-697de9aa0628",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "0055c95d-2032-47b1-92bf-054aee034265",
                        "name": "Guillaume Jacquemet",
                        "external_identifier": "https://orcid.org/0000-0002-9286-920X"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "802eac38-f526-4494-9547-961aa47b1c5f",
                    "roles": [
                        "publisher"
                    ],
                    "organization": {
                        "id": "eb31bf23-9797-425c-b4c4-9206c8507c82",
                        "pref_label": {
                            "en": "Zenodo",
                            "fi": "Zenodo",
                            "sv": "Zenodo"
                        }
                    }
                }
            ],
            "cumulative_state": 0,
            "data_catalog": "urn:nbn:fi:att:data-catalog-abo",
            "description": {
                "en": "This repository includes a StarDist deep learning model and its training dataset designed for segmenting cancer cells perfused over an endothelial cell monolayer captured at 10x magnification. The model was trained on 77 manually annotated images, with the dataset being computationally augmented during training by a factor of 8. The model was trained for 500 epochs and achieved an average F1 Score of 0.968, indicating high accuracy in segmenting cancer cells on endothelial cells. Specifications Model: StarDist for cancer cell segmentation on endothelial cells (10x magnification) Training Dataset: Number of Images: 77 paired brightfield microscopy images and label masks Augmented Dataset: Computational augmentation by a factor of 8 during training Microscope: Nikon Eclipse Ti2-E, 10x objective Data Type: Brightfield microscopy images with manually segmented masks File Format: TIFF (.tif) Brightfield Images: 16-bit Masks: 8-bit or 16-bit Image Size: 1024 x 1022 pixels (pixel size: 1.3148 μm) Training Parameters: Epochs: 500 Patch Size: 992 x 992 pixels Batch Size: 2 Performance: Average F1 Score: 0.968 Average IoU: 0.882 Model Training: Conducted using ZeroCostDL4Mic (https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki) Reference Biorxiv paper"
            },
            "field_of_science": [
                {
                    "id": "e9745cdf-d0e1-4797-8fee-3324e5b2bee2",
                    "url": "http://www.yso.fi/onto/okm-tieteenala/ta1182",
                    "in_scheme": "http://www.yso.fi/onto/okm-tieteenala/conceptscheme",
                    "pref_label": {
                        "en": "Biochemistry, cell and molecular biology",
                        "fi": "Biokemia, solu- ja molekyylibiologia",
                        "sv": "Biokemi, cell- och molekylärbiologi"
                    }
                }
            ],
            "infrastructure": [],
            "issued": "2024-08-12",
            "keyword": [
                "Biochemistry and Cell Biology"
            ],
            "language": [],
            "metadata_owner": {
                "id": "dde6b62a-99e9-49c2-92bc-4a08ae3d9a09",
                "organization": "service_abo"
            },
            "other_identifiers": [],
            "persistent_identifier": "doi:10.5281/zenodo.13304399",
            "pid_generated_by_fairdata": false,
            "projects": [],
            "provenance": [],
            "relation": [],
            "remote_resources": [],
            "spatial": [],
            "state": "published",
            "temporal": [],
            "theme": [],
            "title": {
                "en": "StarDist_BF_cancer_cell_dataset_10x"
            },
            "created": "2025-03-17T05:57:40Z",
            "modified": "2025-03-17T05:57:40Z",
            "dataset_versions": [
                {
                    "id": "9b61bdf0-2e18-46e8-827c-2813d79ca91d",
                    "title": {
                        "en": "StarDist_BF_cancer_cell_dataset_10x"
                    },
                    "persistent_identifier": "doi:10.5281/zenodo.13304399",
                    "state": "published",
                    "created": "2025-03-17T05:57:40Z",
                    "version": 1
                }
            ],
            "published_revision": 1,
            "version": 1,
            "api_version": 3,
            "metadata_repository": "Fairdata"
        },
        {
            "id": "f508aa53-5a51-42f9-b851-14bc09b44af3",
            "access_rights": {
                "id": "6331aefe-bd9f-4ff4-bbe4-5fd3544561f6",
                "license": [
                    {
                        "id": "35b18e72-3819-4ec6-a1be-14624f29d968",
                        "url": "http://uri.suomi.fi/codelist/fairdata/license/code/CC-BY-4.0",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/license",
                        "pref_label": {
                            "en": "Creative Commons Attribution 4.0 International (CC BY 4.0)",
                            "fi": "Creative Commons Nimeä 4.0 Kansainvälinen (CC BY 4.0)"
                        }
                    }
                ],
                "access_type": {
                    "id": "d01ac02c-fc70-4c68-9434-8383cb693ff0",
                    "url": "http://uri.suomi.fi/codelist/fairdata/access_type/code/open",
                    "in_scheme": "http://uri.suomi.fi/codelist/fairdata/access_type",
                    "pref_label": {
                        "en": "Open",
                        "fi": "Avoin"
                    }
                },
                "restriction_grounds": []
            },
            "actors": [
                {
                    "id": "1a4e34c9-2685-4137-a03a-a0144bf51939",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "f0666634-8cc2-470f-94c7-a6f404a09216",
                        "name": "Gautier Follain"
                    },
                    "organization": {
                        "id": "4edd7958-6d63-4a50-af7d-eadb339b79e1",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "11eac644-28de-4a07-8b02-dd66084c6de5",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "fb680ec5-f702-459f-afe0-e3096a8098bf",
                        "name": "Sujan Ghimire",
                        "external_identifier": "https://orcid.org/0000-0003-3660-4300"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "597795ca-7f14-4106-bc78-fc484a9b7096",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "5c2bd717-e5a6-491e-8310-884d9b0ab273",
                        "name": "Joanna Pylvänäinen",
                        "external_identifier": "https://orcid.org/0000-0002-3540-5150"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "8c834ed3-e4cc-4a52-9d2c-92045b67a9e5",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "c7acb246-95f6-4366-80f2-90037d89967b",
                        "name": "Johanna Ivaska"
                    },
                    "organization": {
                        "id": "4edd7958-6d63-4a50-af7d-eadb339b79e1",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "129bd98f-4991-4cc1-adb6-1659c54102fa",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "3e603e8d-19cf-463f-817a-5d864924b78c",
                        "name": "Guillaume Jacquemet",
                        "external_identifier": "https://orcid.org/0000-0002-9286-920X"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "3f6605bb-4116-4879-982d-714374bed5ed",
                    "roles": [
                        "publisher"
                    ],
                    "organization": {
                        "id": "53a1be56-e1f0-4b8b-bdd0-e81e81e5348c",
                        "pref_label": {
                            "en": "Zenodo",
                            "fi": "Zenodo",
                            "sv": "Zenodo"
                        }
                    }
                }
            ],
            "cumulative_state": 0,
            "data_catalog": "urn:nbn:fi:att:data-catalog-abo",
            "description": {
                "en": "This repository includes a StarDist deep learning model designed for segmenting AsPC1 cells labeled with Lifeact from fluorescence microscopy images. The model distinguishes individual AsPC1 cells within clusters and separates them from the background. The model was trained on a small dataset and achieved an Intersection over Union (IoU) score of 0.884 and an F1 Score of 0.967, indicating high accuracy in cell segmentation. Specifications Model: StarDist for segmenting AsPC1 cells in fluorescence microscopy images Training Dataset: Number of Images: 10 paired fluorescence microscopy images and label masks Microscope: Spinning disk confocal microscope (3i CSU-W1) with a 20x objective, NA 0.8 Data Type: Fluorescence microscopy images of the AsPC1 Lifeact channel with manually segmented masks File Format: TIFF (.tif) Fluorescence Images: 16-bit Masks: 8-bit Image Size: 1024 x 1024 pixels (Pixel size: 0.6337 x 0.6337 µm²) Model Capabilities: Segment AsPC1 Cells: Detects individual AsPC1 cells from a cluster and separates them from the background Measure Intensity: Enables measurement of CD44, ICAM1, ICAM2, or Fibronectin intensity under individual cells in respective channels Performance: Average IoU: 0.884 Average F1 Score: 0.967 Model Training: Conducted using ZeroCostDL4Mic (https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki) Reference Biorxiv paper"
            },
            "field_of_science": [
                {
                    "id": "e9745cdf-d0e1-4797-8fee-3324e5b2bee2",
                    "url": "http://www.yso.fi/onto/okm-tieteenala/ta1182",
                    "in_scheme": "http://www.yso.fi/onto/okm-tieteenala/conceptscheme",
                    "pref_label": {
                        "en": "Biochemistry, cell and molecular biology",
                        "fi": "Biokemia, solu- ja molekyylibiologia",
                        "sv": "Biokemi, cell- och molekylärbiologi"
                    }
                }
            ],
            "infrastructure": [],
            "issued": "2024-08-29",
            "keyword": [
                "Biochemistry and Cell Biology"
            ],
            "language": [],
            "metadata_owner": {
                "id": "dde6b62a-99e9-49c2-92bc-4a08ae3d9a09",
                "organization": "service_abo"
            },
            "other_identifiers": [],
            "persistent_identifier": "doi:10.5281/zenodo.13442128",
            "pid_generated_by_fairdata": false,
            "projects": [],
            "provenance": [],
            "relation": [],
            "remote_resources": [],
            "spatial": [],
            "state": "published",
            "temporal": [],
            "theme": [],
            "title": {
                "en": "StarDist_AsPC1_Lifeact"
            },
            "created": "2025-03-17T05:57:38Z",
            "modified": "2025-03-17T05:57:38Z",
            "dataset_versions": [
                {
                    "id": "f508aa53-5a51-42f9-b851-14bc09b44af3",
                    "title": {
                        "en": "StarDist_AsPC1_Lifeact"
                    },
                    "persistent_identifier": "doi:10.5281/zenodo.13442128",
                    "state": "published",
                    "created": "2025-03-17T05:57:38Z",
                    "version": 1
                }
            ],
            "published_revision": 1,
            "version": 1,
            "api_version": 3,
            "metadata_repository": "Fairdata"
        },
        {
            "id": "478de11a-bfaa-444d-bee4-b99620d6d2c4",
            "access_rights": {
                "id": "5ef87a61-8e69-476c-a1bc-1fc7d82db7fd",
                "license": [
                    {
                        "id": "35b18e72-3819-4ec6-a1be-14624f29d968",
                        "url": "http://uri.suomi.fi/codelist/fairdata/license/code/CC-BY-4.0",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/license",
                        "pref_label": {
                            "en": "Creative Commons Attribution 4.0 International (CC BY 4.0)",
                            "fi": "Creative Commons Nimeä 4.0 Kansainvälinen (CC BY 4.0)"
                        }
                    }
                ],
                "access_type": {
                    "id": "d01ac02c-fc70-4c68-9434-8383cb693ff0",
                    "url": "http://uri.suomi.fi/codelist/fairdata/access_type/code/open",
                    "in_scheme": "http://uri.suomi.fi/codelist/fairdata/access_type",
                    "pref_label": {
                        "en": "Open",
                        "fi": "Avoin"
                    }
                },
                "restriction_grounds": []
            },
            "actors": [
                {
                    "id": "057dcdbb-ab4e-4ad5-ae8c-7f9fa399b1c8",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "4ea09a3f-e4e8-4514-92e3-82235f196656",
                        "name": "Gautier Follain"
                    },
                    "organization": {
                        "id": "390bd3cd-dc0e-42c6-a7c8-ad203b23e572",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "b139f4b0-3c2d-4a88-91da-6c24f6e46b98",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "797ac715-174d-4364-a9c8-8606dc947516",
                        "name": "Sujan Ghimire",
                        "external_identifier": "https://orcid.org/0000-0003-3660-4300"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "0b92756c-4c99-4dc4-bfd1-d57e955fdc6c",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "f3067adb-093d-4e95-a9fc-ffbd9cece9a4",
                        "name": "Joanna Pylvänäinen",
                        "external_identifier": "https://orcid.org/0000-0002-3540-5150"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "03533409-f13d-4bb4-ba50-cbc26866b656",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "c1c9c182-8c08-4998-80bb-69ce18cce8db",
                        "name": "Johanna Ivaska"
                    },
                    "organization": {
                        "id": "390bd3cd-dc0e-42c6-a7c8-ad203b23e572",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "22fd0966-412d-40b3-8e37-0f5165c5e891",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "3ab94266-65a1-469b-b25e-4c9589f73c6a",
                        "name": "Guillaume Jacquemet",
                        "external_identifier": "https://orcid.org/0000-0002-9286-920X"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "414b2e64-c1ef-43b7-bf62-adab64141744",
                    "roles": [
                        "publisher"
                    ],
                    "organization": {
                        "id": "866bc91f-4250-49fa-9f72-194989074548",
                        "pref_label": {
                            "en": "Zenodo",
                            "fi": "Zenodo",
                            "sv": "Zenodo"
                        }
                    }
                }
            ],
            "cumulative_state": 0,
            "data_catalog": "urn:nbn:fi:att:data-catalog-abo",
            "description": {
                "en": "This repository contains a StarDist deep learning model designed for segmenting tumor cell nuclei from the DAPI channel in fluorescence microscopy images while excluding HUVEC nuclei. The model was trained to accurately detect individual tumor cell nuclei for subsequent measurement of CD44, ICAM1, ICAM2, or Fibronectin intensity around or under the nuclei. The model achieved an Intersection over Union (IoU) score of 0.558 and an F1 Score of 0.793, reflecting its capability to distinguish tumor cell nuclei from HUVEC nuclei. Specifications Model: StarDist for segmenting tumor cell nuclei from the DAPI fluorescence channel Training Dataset: Number of Images: 48 paired fluorescence microscopy images and label masks Microscope: Spinning disk confocal microscope (3i CSU-W1) with a 20x objective, NA 0.8 Data Type: Fluorescence microscopy images of the DAPI channel with manually segmented masks File Format: TIFF (.tif) Fluorescence Images: 16-bit Masks: 8-bit Image Size: 920 x 920 pixels (Pixel size: 0.6337 x 0.6337 µm²) Model Capabilities: Segment Tumor Cell Nuclei: Detects individual tumor cell nuclei in the DAPI channel while distinguishing them from HUVEC nuclei Measure Intensity: Enables measurement of CD44, ICAM1, ICAM2, or Fibronectin intensity around or under tumor cell nuclei in respective channels Performance: Average IoU: 0.558 Average F1 Score: 0.793 Model Training: Conducted using ZeroCostDL4Mic (https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki) Reference Biorxiv paper"
            },
            "field_of_science": [
                {
                    "id": "e9745cdf-d0e1-4797-8fee-3324e5b2bee2",
                    "url": "http://www.yso.fi/onto/okm-tieteenala/ta1182",
                    "in_scheme": "http://www.yso.fi/onto/okm-tieteenala/conceptscheme",
                    "pref_label": {
                        "en": "Biochemistry, cell and molecular biology",
                        "fi": "Biokemia, solu- ja molekyylibiologia",
                        "sv": "Biokemi, cell- och molekylärbiologi"
                    }
                }
            ],
            "infrastructure": [],
            "issued": "2024-08-29",
            "keyword": [
                "Biochemistry and Cell Biology"
            ],
            "language": [],
            "metadata_owner": {
                "id": "dde6b62a-99e9-49c2-92bc-4a08ae3d9a09",
                "organization": "service_abo"
            },
            "other_identifiers": [],
            "persistent_identifier": "doi:10.5281/zenodo.13443221",
            "pid_generated_by_fairdata": false,
            "projects": [],
            "provenance": [],
            "relation": [],
            "remote_resources": [],
            "spatial": [],
            "state": "published",
            "temporal": [],
            "theme": [],
            "title": {
                "en": "StarDist_TumorCell_nuclei"
            },
            "created": "2025-03-17T05:57:36Z",
            "modified": "2025-03-17T05:57:36Z",
            "dataset_versions": [
                {
                    "id": "478de11a-bfaa-444d-bee4-b99620d6d2c4",
                    "title": {
                        "en": "StarDist_TumorCell_nuclei"
                    },
                    "persistent_identifier": "doi:10.5281/zenodo.13443221",
                    "state": "published",
                    "created": "2025-03-17T05:57:36Z",
                    "version": 1
                }
            ],
            "published_revision": 1,
            "version": 1,
            "api_version": 3,
            "metadata_repository": "Fairdata"
        },
        {
            "id": "153bdf74-d740-43d6-87b8-b0bc189295f2",
            "access_rights": {
                "id": "7b8ec67a-7eb7-4819-9c44-83b70a7adff4",
                "license": [
                    {
                        "id": "60ce96ab-a581-4225-a652-bad746a435a2",
                        "url": "http://uri.suomi.fi/codelist/fairdata/license/code/notspecified",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/license",
                        "pref_label": {
                            "en": "License Not Specified",
                            "fi": "Ei määritelty"
                        }
                    }
                ],
                "access_type": {
                    "id": "729ffd9f-6d7a-40e9-aa97-a363a16fd113",
                    "url": "http://uri.suomi.fi/codelist/fairdata/access_type/code/restricted",
                    "in_scheme": "http://uri.suomi.fi/codelist/fairdata/access_type",
                    "pref_label": {
                        "en": "Restricted use",
                        "fi": "Saatavuutta rajoitettu"
                    }
                },
                "restriction_grounds": [
                    {
                        "id": "0ed3a2e1-6c11-4278-af67-c6713f838ecd",
                        "url": "http://uri.suomi.fi/codelist/fairdata/restriction_grounds/code/other",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/restriction_grounds",
                        "pref_label": {
                            "en": "Restricted access due to other reasons",
                            "fi": "Saatavuutta rajoitettu muulla perusteella",
                            "sv": "Begränsad åtkomst av övriga skäl"
                        }
                    }
                ]
            },
            "actors": [
                {
                    "id": "eae9cbb0-3f9f-4626-8b40-be801b861a92",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "62a41085-add6-4efd-8377-dc9c720151d8",
                        "name": "Tomi Airenne",
                        "external_identifier": "https://orcid.org/0000-0001-9645-8670"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "2c5e7402-b19a-48e0-bb23-aae1ed1b2e20",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "da23f049-b8e5-4bcf-9913-50ce5b7f505b",
                        "name": "Chiara Bosetti"
                    },
                    "organization": {
                        "id": "18f83fe9-1bad-48cb-a264-10ce18bcbc71",
                        "pref_label": {
                            "en": "University of Oulu",
                            "fi": "Oulun yliopisto",
                            "sv": "University of Oulu"
                        },
                        "external_identifier": "https://ror.org/03yj89h83"
                    }
                },
                {
                    "id": "e4787289-af35-4fc8-a494-07830725e457",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "e42d9754-3984-4695-90a8-d6f5854e3ff5",
                        "name": "Subhadra Dalwani"
                    },
                    "organization": {
                        "id": "18f83fe9-1bad-48cb-a264-10ce18bcbc71",
                        "pref_label": {
                            "en": "University of Oulu",
                            "fi": "Oulun yliopisto",
                            "sv": "University of Oulu"
                        },
                        "external_identifier": "https://ror.org/03yj89h83"
                    }
                },
                {
                    "id": "ac32ba23-ff65-41a1-98af-874f12ae4112",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "a52191fb-4091-488c-99a7-c894241ab10f",
                        "name": "Saurabh Dhakar"
                    },
                    "organization": {
                        "id": "18f83fe9-1bad-48cb-a264-10ce18bcbc71",
                        "pref_label": {
                            "en": "University of Oulu",
                            "fi": "Oulun yliopisto",
                            "sv": "University of Oulu"
                        },
                        "external_identifier": "https://ror.org/03yj89h83"
                    }
                },
                {
                    "id": "3dee8501-c8d9-4cda-b4be-70f792fb8b0d",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "881bcac1-aefb-4115-b7d7-d7b28a9e311e",
                        "name": "Thi Hoai Men Duong"
                    },
                    "organization": {
                        "id": "18f83fe9-1bad-48cb-a264-10ce18bcbc71",
                        "pref_label": {
                            "en": "University of Oulu",
                            "fi": "Oulun yliopisto",
                            "sv": "University of Oulu"
                        },
                        "external_identifier": "https://ror.org/03yj89h83"
                    }
                },
                {
                    "id": "8a9ed228-a550-4977-b187-bcd51bdf9303",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "8bac0c6a-058b-45c6-9825-70d383792ab7",
                        "name": "Mikko Huhtala"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "499e73f6-84f8-469a-8b65-26e8fd5daf8c",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "a5dd12ac-6bc5-4873-95a9-96a1a327d3c5",
                        "name": "Mikael Ilomäki"
                    },
                    "organization": {
                        "id": "df4ca452-8885-48df-8f18-0fe7b8e2a63e",
                        "pref_label": {
                            "en": "Abo Akademi University"
                        }
                    }
                },
                {
                    "id": "7ab380f3-5ea5-48de-a176-f787b94b344f",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "b90decb4-3262-4d24-861b-e78b799e532f",
                        "name": "Tommi  Kajander"
                    },
                    "organization": {
                        "id": "d6ab7633-ae40-4798-af1f-dc39daaff059",
                        "pref_label": {
                            "en": "University of Helsinki",
                            "fi": "Helsingin yliopisto",
                            "sv": "Helsingfors universitet"
                        },
                        "external_identifier": "https://ror.org/040af2s02"
                    }
                },
                {
                    "id": "d801acd5-f7ab-49b0-a771-2104e25a2dbc",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "6c6a9296-f9a7-407c-93cb-9f9dcdf1f875",
                        "name": "Kristian Koski"
                    },
                    "organization": {
                        "id": "18f83fe9-1bad-48cb-a264-10ce18bcbc71",
                        "pref_label": {
                            "en": "University of Oulu",
                            "fi": "Oulun yliopisto",
                            "sv": "University of Oulu"
                        },
                        "external_identifier": "https://ror.org/03yj89h83"
                    }
                },
                {
                    "id": "a4d4fdcc-6e28-4167-9da0-a0748cdd0d42",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "19152d2d-433a-4eb1-9468-3dbb9455c92d",
                        "name": "Lari Lehtio"
                    },
                    "organization": {
                        "id": "18f83fe9-1bad-48cb-a264-10ce18bcbc71",
                        "pref_label": {
                            "en": "University of Oulu",
                            "fi": "Oulun yliopisto",
                            "sv": "University of Oulu"
                        },
                        "external_identifier": "https://ror.org/03yj89h83"
                    }
                },
                {
                    "id": "83801bd9-5e75-4aad-88f8-45f091851968",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "a6069ae6-ea0c-4005-bb7a-a2b7309dab01",
                        "name": "Johan Pääkkönen"
                    },
                    "organization": {
                        "id": "18f83fe9-1bad-48cb-a264-10ce18bcbc71",
                        "pref_label": {
                            "en": "University of Oulu",
                            "fi": "Oulun yliopisto",
                            "sv": "University of Oulu"
                        },
                        "external_identifier": "https://ror.org/03yj89h83"
                    }
                },
                {
                    "id": "3671cb10-19c6-4cf7-8baa-09b46e9aa0a5",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "c619fc67-0046-4a19-95a1-9e8a51c18d4a",
                        "name": "Abhinandan Venkatesha Murthy"
                    },
                    "organization": {
                        "id": "d6ab7633-ae40-4798-af1f-dc39daaff059",
                        "pref_label": {
                            "en": "University of Helsinki",
                            "fi": "Helsingin yliopisto",
                            "sv": "Helsingfors universitet"
                        },
                        "external_identifier": "https://ror.org/040af2s02"
                    }
                },
                {
                    "id": "182e0acf-ce37-4a76-a52a-dd57b340b14c",
                    "roles": [
                        "contributor"
                    ],
                    "person": {
                        "id": "c6b50b2a-5d64-4354-b5a9-cf5b6f7a9822",
                        "name": "Igor Melnikov"
                    },
                    "organization": {
                        "id": "39a257d3-87b0-4528-99c7-bcabcab555f8",
                        "pref_label": {
                            "en": "ESRF,CS 40220,38043 GRENOBLE Cedex 9,FRANCE,38043,GRENOBLE,FRANCE"
                        }
                    }
                },
                {
                    "id": "95d20832-c038-48c7-a03c-d4025db9d5ef",
                    "roles": [
                        "publisher"
                    ],
                    "organization": {
                        "id": "d1d792f3-d63a-4f8b-9e48-4bf1420b8517",
                        "pref_label": {
                            "en": "European Synchrotron Radiation Facility",
                            "fi": "European Synchrotron Radiation Facility",
                            "sv": "European Synchrotron Radiation Facility"
                        }
                    }
                }
            ],
            "cumulative_state": 0,
            "data_catalog": "urn:nbn:fi:att:data-catalog-abo",
            "description": {
                "en": "The Finnish BAG encompasses 24 groups active in crystallography in Finland. The projects vary widely and include membrane proteins and protein complexes, other proteins involved in disease and antibiotics and drug development and discovery (ADP-ribosylation and several oncogenic proteins including kinases, biocatalysis, endoplasmic regulation and protein secretion) and several pathogen proteins and various enzyme targets and e.g. studies on phytochrome photoreceptors and complexes involved in actin dynamics regulation as well as membrane protein targets. Overall the BAG serves the national needs for highly variable projects, with different biological and biotechnological applications. Several project will benefit from microfocus beam lines and tunable wavelength options, others benefit from quick robust screening by MASSIF."
            },
            "field_of_science": [
                {
                    "id": "e9745cdf-d0e1-4797-8fee-3324e5b2bee2",
                    "url": "http://www.yso.fi/onto/okm-tieteenala/ta1182",
                    "in_scheme": "http://www.yso.fi/onto/okm-tieteenala/conceptscheme",
                    "pref_label": {
                        "en": "Biochemistry, cell and molecular biology",
                        "fi": "Biokemia, solu- ja molekyylibiologia",
                        "sv": "Biokemi, cell- och molekylärbiologi"
                    }
                }
            ],
            "infrastructure": [],
            "issued": "2027-01-01",
            "keyword": [
                "x-ray probe",
                "Macromolecular Crystallography",
                "MX-2640",
                "ID30A-3"
            ],
            "language": [],
            "metadata_owner": {
                "id": "dde6b62a-99e9-49c2-92bc-4a08ae3d9a09",
                "organization": "service_abo"
            },
            "other_identifiers": [],
            "persistent_identifier": "doi:10.15151/esrf-es-1830152652",
            "pid_generated_by_fairdata": false,
            "projects": [],
            "provenance": [],
            "relation": [],
            "remote_resources": [],
            "spatial": [],
            "state": "published",
            "temporal": [],
            "theme": [],
            "title": {
                "en": "FInnish National Protein Crystallography Consortium"
            },
            "created": "2025-03-17T05:57:34Z",
            "modified": "2025-03-17T05:57:34Z",
            "dataset_versions": [
                {
                    "id": "153bdf74-d740-43d6-87b8-b0bc189295f2",
                    "title": {
                        "en": "FInnish National Protein Crystallography Consortium"
                    },
                    "persistent_identifier": "doi:10.15151/esrf-es-1830152652",
                    "state": "published",
                    "created": "2025-03-17T05:57:34Z",
                    "version": 1
                }
            ],
            "published_revision": 1,
            "version": 1,
            "api_version": 3,
            "metadata_repository": "Fairdata"
        },
        {
            "id": "3d4c2a18-1da2-483d-a18d-d5bcac5f53f1",
            "access_rights": {
                "id": "f378a5ee-0e23-4dc1-af5a-62f88b7f7e05",
                "license": [
                    {
                        "id": "35b18e72-3819-4ec6-a1be-14624f29d968",
                        "url": "http://uri.suomi.fi/codelist/fairdata/license/code/CC-BY-4.0",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/license",
                        "pref_label": {
                            "en": "Creative Commons Attribution 4.0 International (CC BY 4.0)",
                            "fi": "Creative Commons Nimeä 4.0 Kansainvälinen (CC BY 4.0)"
                        }
                    }
                ],
                "access_type": {
                    "id": "d01ac02c-fc70-4c68-9434-8383cb693ff0",
                    "url": "http://uri.suomi.fi/codelist/fairdata/access_type/code/open",
                    "in_scheme": "http://uri.suomi.fi/codelist/fairdata/access_type",
                    "pref_label": {
                        "en": "Open",
                        "fi": "Avoin"
                    }
                },
                "restriction_grounds": []
            },
            "actors": [
                {
                    "id": "2fa798c5-bf13-462d-8446-21058041807e",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "8749d4e5-57c5-4569-b758-8c392b600d9f",
                        "name": "Gautier Follain"
                    },
                    "organization": {
                        "id": "0f9675d8-e202-4a03-8bb7-9956e6cc1c17",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "8013f803-b29a-4f7c-b0c1-6a69d91b4db4",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "3dc68e05-8d31-4292-bf43-5e96574607b8",
                        "name": "Sujan Ghimire",
                        "external_identifier": "https://orcid.org/0000-0003-3660-4300"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "b60f405a-c722-43b3-95f5-2cf65f19fa98",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "607675e0-9181-4db2-8239-3164b7eaa167",
                        "name": "Joanna Pylvänäinen",
                        "external_identifier": "https://orcid.org/0000-0002-3540-5150"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "5087c9ff-811a-4658-8399-10cdfa5b1f2a",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "8dc701d0-3ed8-45f4-8763-d0f3ba98e926",
                        "name": "Johanna Ivaska"
                    },
                    "organization": {
                        "id": "0f9675d8-e202-4a03-8bb7-9956e6cc1c17",
                        "pref_label": {
                            "en": "University of Turku"
                        }
                    }
                },
                {
                    "id": "7dad9840-b438-4059-a5f5-c060ec01939f",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "aaaff202-41df-4bb7-94c3-1efbb76e3eee",
                        "name": "Guillaume Jacquemet",
                        "external_identifier": "https://orcid.org/0000-0002-9286-920X"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "629f1b58-e1ee-414f-900f-54abb9d7993e",
                    "roles": [
                        "publisher"
                    ],
                    "organization": {
                        "id": "30393982-4946-4a69-9328-9a10caf99f3b",
                        "pref_label": {
                            "en": "Zenodo",
                            "fi": "Zenodo",
                            "sv": "Zenodo"
                        }
                    }
                }
            ],
            "cumulative_state": 0,
            "data_catalog": "urn:nbn:fi:att:data-catalog-abo",
            "description": {
                "en": "This repository contains a StarDist deep learning model designed for segmenting MiaPaCa2 cells from the CD44 channel in fluorescence microscopy images. The model is capable of accurately segmenting individual MiaPaCa2 cells while excluding HUVECs. Trained on a small dataset, the model achieved an Intersection over Union (IoU) score of 0.884 and an F1 Score of 0.950, indicating high precision in cell segmentation. Specifications Model: StarDist for segmenting MiaPaCa2 cells from the CD44 fluorescence channel Training Dataset: Number of Images: 8 paired fluorescence microscopy images and label masks Microscope: Spinning disk confocal microscope (3i CSU-W1) with a 20x objective, NA 0.8 Data Type: Fluorescence microscopy images of the CD44 channel, obtained after immunofluorescence staining with primary and secondary antibodies and manually segmented masks File Format: TIFF (.tif) Fluorescence Images: 16-bit Masks: 8-bit Image Size: 920 x 920 pixels (Pixel size: 0.6337 x 0.6337 µm²) Model Capabilities: Segment MiaPaCa2 Cells: Accurately detects individual MiaPaCa2 cells while ignoring HUVECs Measure CD44 Intensity: Allows for the measurement of CD44 intensity around MiaPaCa2 cells, specifically from the CD44 channel Performance: Average IoU: 0.884 Average F1 Score: 0.950 Model Training: Conducted using ZeroCostDL4Mic (https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki) Reference Biorxiv paper"
            },
            "field_of_science": [
                {
                    "id": "e9745cdf-d0e1-4797-8fee-3324e5b2bee2",
                    "url": "http://www.yso.fi/onto/okm-tieteenala/ta1182",
                    "in_scheme": "http://www.yso.fi/onto/okm-tieteenala/conceptscheme",
                    "pref_label": {
                        "en": "Biochemistry, cell and molecular biology",
                        "fi": "Biokemia, solu- ja molekyylibiologia",
                        "sv": "Biokemi, cell- och molekylärbiologi"
                    }
                }
            ],
            "infrastructure": [],
            "issued": "2024-08-29",
            "keyword": [
                "Biochemistry and Cell Biology"
            ],
            "language": [],
            "metadata_owner": {
                "id": "dde6b62a-99e9-49c2-92bc-4a08ae3d9a09",
                "organization": "service_abo"
            },
            "other_identifiers": [],
            "persistent_identifier": "doi:10.5281/zenodo.13442877",
            "pid_generated_by_fairdata": false,
            "projects": [],
            "provenance": [],
            "relation": [],
            "remote_resources": [],
            "spatial": [],
            "state": "published",
            "temporal": [],
            "theme": [],
            "title": {
                "en": "Stardist_MiaPaCa2_from_CD44"
            },
            "created": "2025-03-17T05:57:32Z",
            "modified": "2025-03-17T05:57:32Z",
            "dataset_versions": [
                {
                    "id": "3d4c2a18-1da2-483d-a18d-d5bcac5f53f1",
                    "title": {
                        "en": "Stardist_MiaPaCa2_from_CD44"
                    },
                    "persistent_identifier": "doi:10.5281/zenodo.13442877",
                    "state": "published",
                    "created": "2025-03-17T05:57:32Z",
                    "version": 1
                }
            ],
            "published_revision": 1,
            "version": 1,
            "api_version": 3,
            "metadata_repository": "Fairdata"
        },
        {
            "id": "43f43b0e-70c5-40bc-951a-360b52129809",
            "access_rights": {
                "id": "76642d1b-0464-49de-bcbc-53415e4edca8",
                "license": [
                    {
                        "id": "9f8e151c-af07-44f6-8104-a30b68fc2b3c",
                        "url": "http://uri.suomi.fi/codelist/fairdata/license/code/CC0-1.0",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/license",
                        "pref_label": {
                            "en": "Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain Dedication",
                            "fi": "Creative Commons Yleismaailmallinen (CC0 1.0) Public Domain -lausuma"
                        }
                    }
                ],
                "access_type": {
                    "id": "d01ac02c-fc70-4c68-9434-8383cb693ff0",
                    "url": "http://uri.suomi.fi/codelist/fairdata/access_type/code/open",
                    "in_scheme": "http://uri.suomi.fi/codelist/fairdata/access_type",
                    "pref_label": {
                        "en": "Open",
                        "fi": "Avoin"
                    }
                },
                "restriction_grounds": []
            },
            "actors": [
                {
                    "id": "97dd5d72-5d01-4ccf-b7bc-997711d34e3b",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "50166745-0f23-4209-b247-b3d7d354e1a4",
                        "name": "Carsten Anckar",
                        "external_identifier": "https://orcid.org/0000-0003-3812-2014"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "31cc7c0c-d184-4871-8d8d-fcb55523f49a",
                    "roles": [
                        "publisher"
                    ],
                    "organization": {
                        "id": "c08eecef-0871-4219-a73f-9c209d9f9f52",
                        "pref_label": {
                            "en": "Harvard Dataverse",
                            "fi": "Harvard Dataverse",
                            "sv": "Harvard Dataverse"
                        }
                    }
                }
            ],
            "cumulative_state": 0,
            "data_catalog": "urn:nbn:fi:att:data-catalog-abo",
            "description": {
                "en": "We provide a yearly categorization of death penalty status as well as changes of the status in the world. The database covers the period 1800-2022 for all currently independent countries in the world. (2024-05-20)"
            },
            "field_of_science": [
                {
                    "id": "df60b812-8951-4f38-944d-a1eff560ad85",
                    "url": "http://www.yso.fi/onto/okm-tieteenala/ta517",
                    "in_scheme": "http://www.yso.fi/onto/okm-tieteenala/conceptscheme",
                    "pref_label": {
                        "en": "Political science",
                        "fi": "Valtio-oppi, hallintotiede",
                        "sv": "Statsvetenskap"
                    }
                }
            ],
            "infrastructure": [],
            "issued": "2024-06-04",
            "keyword": [
                "death penalty",
                "legislation"
            ],
            "language": [],
            "metadata_owner": {
                "id": "dde6b62a-99e9-49c2-92bc-4a08ae3d9a09",
                "organization": "service_abo"
            },
            "other_identifiers": [],
            "persistent_identifier": "doi:10.7910/DVN/LI3WYK",
            "pid_generated_by_fairdata": false,
            "projects": [],
            "provenance": [],
            "relation": [],
            "remote_resources": [],
            "spatial": [],
            "state": "published",
            "temporal": [],
            "theme": [],
            "title": {
                "en": "Comparative Death Penalty Database",
                "sv": "Comparative Death Penalty Database"
            },
            "created": "2025-03-17T05:57:29Z",
            "modified": "2025-03-17T05:57:29Z",
            "dataset_versions": [
                {
                    "id": "43f43b0e-70c5-40bc-951a-360b52129809",
                    "title": {
                        "en": "Comparative Death Penalty Database",
                        "sv": "Comparative Death Penalty Database"
                    },
                    "persistent_identifier": "doi:10.7910/DVN/LI3WYK",
                    "state": "published",
                    "created": "2025-03-17T05:57:29Z",
                    "version": 1
                }
            ],
            "published_revision": 1,
            "version": 1,
            "api_version": 3,
            "metadata_repository": "Fairdata"
        },
        {
            "id": "d549cbeb-f8dc-4949-a841-108b0973ad68",
            "access_rights": {
                "id": "9ac77e17-5029-417f-bd8e-abaefc2e8fc3",
                "license": [
                    {
                        "id": "6142d0c6-945d-4085-b9f7-81e52afa253b",
                        "url": "http://uri.suomi.fi/codelist/fairdata/license/code/other",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/license",
                        "pref_label": {
                            "en": "Other",
                            "fi": "Muu"
                        }
                    }
                ],
                "access_type": {
                    "id": "729ffd9f-6d7a-40e9-aa97-a363a16fd113",
                    "url": "http://uri.suomi.fi/codelist/fairdata/access_type/code/restricted",
                    "in_scheme": "http://uri.suomi.fi/codelist/fairdata/access_type",
                    "pref_label": {
                        "en": "Restricted use",
                        "fi": "Saatavuutta rajoitettu"
                    }
                },
                "restriction_grounds": [
                    {
                        "id": "0ed3a2e1-6c11-4278-af67-c6713f838ecd",
                        "url": "http://uri.suomi.fi/codelist/fairdata/restriction_grounds/code/other",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/restriction_grounds",
                        "pref_label": {
                            "en": "Restricted access due to other reasons",
                            "fi": "Saatavuutta rajoitettu muulla perusteella",
                            "sv": "Begränsad åtkomst av övriga skäl"
                        }
                    }
                ]
            },
            "actors": [
                {
                    "id": "ccee62e3-9c97-4911-b177-ce7b82e28762",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "72588e18-fc63-46e9-aea2-ea62e42bb67b",
                        "name": "Kimmo Grönlund",
                        "external_identifier": "https://orcid.org/0000-0001-9386-5043"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "eee05183-c97c-4273-8983-72c8eda22752",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "50f51939-02c9-4a8a-bb99-5a39e421d52a",
                        "name": "Kaisa Herne"
                    },
                    "organization": {
                        "id": "b5bad1a6-4578-438e-a928-c3d431a7e865",
                        "pref_label": {
                            "en": "University of Turku. Department of Political Science"
                        }
                    }
                },
                {
                    "id": "e458097c-abb1-4efc-a111-a37533939f66",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "a47a6076-3f3d-441d-b1fc-6a36e6471620",
                        "name": "Maija Setälä"
                    },
                    "organization": {
                        "id": "b5bad1a6-4578-438e-a928-c3d431a7e865",
                        "pref_label": {
                            "en": "University of Turku. Department of Political Science"
                        }
                    }
                },
                {
                    "id": "7e6b6acf-d49f-4cd9-9a7c-58cdd8f6f3d1",
                    "roles": [
                        "publisher"
                    ],
                    "organization": {
                        "id": "168aa9b2-5ca3-4e61-8783-2c80a27c4af7",
                        "pref_label": {
                            "en": "Tietoarkisto",
                            "fi": "Tietoarkisto",
                            "sv": "Tietoarkisto"
                        }
                    }
                }
            ],
            "cumulative_state": 0,
            "data_catalog": "urn:nbn:fi:att:data-catalog-abo",
            "description": {
                "en": "The data contain the responses of five surveys conducted in connection with the deliberative experiment called Citizen Deliberation organised by the Interdisciplinary Centre of Excellence \"Democracy: a Citizen Perspective\", at the Åbo Akademi University. The Citizen Deliberation was en experiment on democratic deliberation, which culminated in the actual deliberation day organised in Turku on the 18th of November 2006. The topic of the discussion was: \"Should a sixth nuclear power plant be built in Finland?\" Before the actual deliberation day, the participants received balanced information on nuclear energy, and they were also given an opportunity to hear experts' views on the topic. The discussion was conducted under guidance in small groups. The surveys were conducted in three waves: in September 2006, on the 18th of November 2006, and in February 2007. In September, 2,500 randomly sampled people from Turku region were sent a survey and an invitation to the Citizen Deliberation event. The survey contained questions on nuclear power, energy, social participation, and political activity. In addition, socio-economic background variables were included in the September questionnaire. The November wave contained three surveys, which were conducted at the beginning, during, and at the end of the deliberative discussion. In the first survey, the respondents participating in the discussion were asked about their views on energy issues and general knowledge on political issues. The respondents replied to the second survey after familiarising themselves with the balanced information on nuclear energy and hearing the experts, but before the group discussions. The third survey was presented to the respondents at the end of the event, and it contained the same questions that were posed at the beginning of the discussion and in September. In addition, the respondents' experiences on the Citizen Deliberation were charted. The number of respondents in the November surveys was 135. In February, the participants of the Citizen Deliberation and the respondents volunteered in the September survey were sent a follow-up questionnaire, which included mostly the same questions as the first data collection round, but there were also additional questions for those who had participated in the Citizen Deliberation event. Background variables included the respondent's gender, age, mother tongue, municipality of residence, year of birth, marital status, education, occupational group, economic activity, household size, and gross income."
            },
            "field_of_science": [
                {
                    "id": "df60b812-8951-4f38-944d-a1eff560ad85",
                    "url": "http://www.yso.fi/onto/okm-tieteenala/ta517",
                    "in_scheme": "http://www.yso.fi/onto/okm-tieteenala/conceptscheme",
                    "pref_label": {
                        "en": "Political science",
                        "fi": "Valtio-oppi, hallintotiede",
                        "sv": "Statsvetenskap"
                    }
                }
            ],
            "infrastructure": [],
            "issued": "2009-12-18",
            "keyword": [
                "political action",
                "Poliittinen käyttäytyminen, poliittiset asenteet ja mielipiteet",
                "Energy and natural resources",
                "Social sciences",
                "energia",
                "ydinvoimalat",
                "attitudes",
                "asenteet",
                "Energia- ja luonnonvarat",
                "Political behaviour and attitudes",
                "nuclear power stations",
                "nuclear energy",
                "democracy",
                "ydinenergia",
                "organizations",
                "julkinen keskustelu",
                "public opinion",
                "demokratia",
                "järjestöt",
                "poliittinen toiminta",
                "energy"
            ],
            "language": [],
            "metadata_owner": {
                "id": "dde6b62a-99e9-49c2-92bc-4a08ae3d9a09",
                "organization": "service_abo"
            },
            "other_identifiers": [],
            "persistent_identifier": "doi:10.60686/t-fsd2355",
            "pid_generated_by_fairdata": false,
            "projects": [],
            "provenance": [],
            "relation": [],
            "remote_resources": [],
            "spatial": [],
            "state": "published",
            "temporal": [],
            "theme": [],
            "title": {
                "en": "Deliberative Discussion on Nuclear Power 2006"
            },
            "created": "2025-03-17T05:57:27Z",
            "modified": "2025-03-17T05:57:27Z",
            "dataset_versions": [
                {
                    "id": "d549cbeb-f8dc-4949-a841-108b0973ad68",
                    "title": {
                        "en": "Deliberative Discussion on Nuclear Power 2006"
                    },
                    "persistent_identifier": "doi:10.60686/t-fsd2355",
                    "state": "published",
                    "created": "2025-03-17T05:57:27Z",
                    "version": 1
                }
            ],
            "published_revision": 1,
            "version": 1,
            "api_version": 3,
            "metadata_repository": "Fairdata"
        },
        {
            "id": "c178d6fc-23f2-4fe0-9cf4-a7de7e94cb65",
            "access_rights": {
                "id": "2d7b5dc8-1914-40f5-9fdd-dde0711bb476",
                "license": [
                    {
                        "id": "35b18e72-3819-4ec6-a1be-14624f29d968",
                        "url": "http://uri.suomi.fi/codelist/fairdata/license/code/CC-BY-4.0",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/license",
                        "pref_label": {
                            "en": "Creative Commons Attribution 4.0 International (CC BY 4.0)",
                            "fi": "Creative Commons Nimeä 4.0 Kansainvälinen (CC BY 4.0)"
                        }
                    }
                ],
                "access_type": {
                    "id": "d01ac02c-fc70-4c68-9434-8383cb693ff0",
                    "url": "http://uri.suomi.fi/codelist/fairdata/access_type/code/open",
                    "in_scheme": "http://uri.suomi.fi/codelist/fairdata/access_type",
                    "pref_label": {
                        "en": "Open",
                        "fi": "Avoin"
                    }
                },
                "restriction_grounds": []
            },
            "actors": [
                {
                    "id": "f29d4cd2-3693-477f-8b0c-711f10201425",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "3e44c1f0-4e06-4a28-a14e-890c7b10dd24",
                        "name": "C. M. (Cecilia) Sahlgren",
                        "external_identifier": "https://orcid.org/0000-0003-3350-4937"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "883b7f35-902b-450e-8d33-b6c15c356973",
                    "roles": [
                        "publisher"
                    ],
                    "organization": {
                        "id": "ad193e43-936d-4670-928e-e9d6ba2d1266",
                        "pref_label": {
                            "en": "4TU.ResearchData",
                            "fi": "4TU.ResearchData",
                            "sv": "4TU.ResearchData"
                        }
                    }
                }
            ],
            "cumulative_state": 0,
            "data_catalog": "urn:nbn:fi:att:data-catalog-abo",
            "description": {
                "en": "The data and resulting publication describe the fabrication and characterization of an artery-on-chip: a biomimetic microfluidic device for in vitro studies of endothelial cells and vascular smooth muscle cells under hemodynamic conditions. The dataset consists of bioimaging, quantitative real-time PCR (qPCR) and directionality analysis data."
            },
            "field_of_science": [
                {
                    "id": "e9745cdf-d0e1-4797-8fee-3324e5b2bee2",
                    "url": "http://www.yso.fi/onto/okm-tieteenala/ta1182",
                    "in_scheme": "http://www.yso.fi/onto/okm-tieteenala/conceptscheme",
                    "pref_label": {
                        "en": "Biochemistry, cell and molecular biology",
                        "fi": "Biokemia, solu- ja molekyylibiologia",
                        "sv": "Biokemi, cell- och molekylärbiologi"
                    }
                }
            ],
            "infrastructure": [],
            "issued": "2020-09-02",
            "keyword": [
                "Biomedical Engineering",
                "Endothelial Cells",
                "FOS: Biological sciences",
                "Biomimetics",
                "FOS: Medical engineering",
                "Biochemistry and Cell Biology",
                "Vascular smooth muscle cells (VSMCs)",
                "Microfluidics",
                "hemodynamics",
                "Time: 2016-2018"
            ],
            "language": [],
            "metadata_owner": {
                "id": "dde6b62a-99e9-49c2-92bc-4a08ae3d9a09",
                "organization": "service_abo"
            },
            "other_identifiers": [],
            "persistent_identifier": "doi:10.4121/12854756.v1",
            "pid_generated_by_fairdata": false,
            "projects": [],
            "provenance": [],
            "relation": [],
            "remote_resources": [],
            "spatial": [],
            "state": "published",
            "temporal": [],
            "theme": [],
            "title": {
                "en": "Data underlying the publication \"A biomimetic microfluidic model to study signalling between endothelial and vascular smooth muscle cells under hemodynamic conditions\""
            },
            "created": "2025-03-17T05:57:25Z",
            "modified": "2025-03-17T05:57:25Z",
            "dataset_versions": [
                {
                    "id": "c178d6fc-23f2-4fe0-9cf4-a7de7e94cb65",
                    "title": {
                        "en": "Data underlying the publication \"A biomimetic microfluidic model to study signalling between endothelial and vascular smooth muscle cells under hemodynamic conditions\""
                    },
                    "persistent_identifier": "doi:10.4121/12854756.v1",
                    "state": "published",
                    "created": "2025-03-17T05:57:25Z",
                    "version": 1
                }
            ],
            "published_revision": 1,
            "version": 1,
            "api_version": 3,
            "metadata_repository": "Fairdata"
        },
        {
            "id": "c93b18b0-3e0b-449c-ba94-59dc05d49e92",
            "access_rights": {
                "id": "5f01b503-1af0-4311-8a7f-c051429ec32a",
                "license": [
                    {
                        "id": "35b18e72-3819-4ec6-a1be-14624f29d968",
                        "url": "http://uri.suomi.fi/codelist/fairdata/license/code/CC-BY-4.0",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/license",
                        "pref_label": {
                            "en": "Creative Commons Attribution 4.0 International (CC BY 4.0)",
                            "fi": "Creative Commons Nimeä 4.0 Kansainvälinen (CC BY 4.0)"
                        }
                    }
                ],
                "access_type": {
                    "id": "d01ac02c-fc70-4c68-9434-8383cb693ff0",
                    "url": "http://uri.suomi.fi/codelist/fairdata/access_type/code/open",
                    "in_scheme": "http://uri.suomi.fi/codelist/fairdata/access_type",
                    "pref_label": {
                        "en": "Open",
                        "fi": "Avoin"
                    }
                },
                "restriction_grounds": []
            },
            "actors": [
                {
                    "id": "11acf3d9-ff27-4c5e-92ce-28271f09dc22",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "0456caae-e4cf-4007-bd13-3d02bfab0c32",
                        "name": "C. M. (Cecilia) Sahlgren",
                        "external_identifier": "https://orcid.org/0000-0003-3350-4937"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "7506f951-39ad-4ec3-80e6-2ecd6d86ed37",
                    "roles": [
                        "publisher"
                    ],
                    "organization": {
                        "id": "320d1a21-8656-4345-8cf4-dc1fd88e42c9",
                        "pref_label": {
                            "en": "4TU.ResearchData",
                            "fi": "4TU.ResearchData",
                            "sv": "4TU.ResearchData"
                        }
                    }
                }
            ],
            "cumulative_state": 0,
            "data_catalog": "urn:nbn:fi:att:data-catalog-abo",
            "description": {
                "en": "Spatial regulation of angiogenesis is important for the generation of functional engineered vasculature and the Notch ligands Jag1 and Dll4 are known to regulate endothelial sprouting. In this project, <em>in vitro </em>and <em>in silico </em>models were used to analyze the ability of micropatterned Jag1 and Dll4 to spatially control the sprouting process. Dll4 patterns, but not Jag1 patterns, were found to elicit spatial control and computational simulations suggest different timing of Notch activation by Jag1 and Dll4 to be the reason for their distinct effects. The more potent spatial control of sprouting by Dll4 in comparison to Jag1 could be exploited as a tool in vascular engineering and regenerative medicine.  This dataset contains computational modeling data simulating cell-cell signaling mediated by Notch ligands Jag1 and Dll4 during controlled endothelial sprouting."
            },
            "field_of_science": [
                {
                    "id": "e9745cdf-d0e1-4797-8fee-3324e5b2bee2",
                    "url": "http://www.yso.fi/onto/okm-tieteenala/ta1182",
                    "in_scheme": "http://www.yso.fi/onto/okm-tieteenala/conceptscheme",
                    "pref_label": {
                        "en": "Biochemistry, cell and molecular biology",
                        "fi": "Biokemia, solu- ja molekyylibiologia",
                        "sv": "Biokemi, cell- och molekylärbiologi"
                    }
                }
            ],
            "infrastructure": [],
            "issued": "2022-05-06",
            "keyword": [
                "endothelial sprouting",
                "Biomedical Engineering",
                "Notch ligand Jag1",
                "FOS: Biological sciences",
                "micropatterning",
                "Notch ligand Dll4",
                "FOS: Medical engineering",
                "Biochemistry and Cell Biology"
            ],
            "language": [],
            "metadata_owner": {
                "id": "dde6b62a-99e9-49c2-92bc-4a08ae3d9a09",
                "organization": "service_abo"
            },
            "other_identifiers": [],
            "persistent_identifier": "doi:10.4121/19235793",
            "pid_generated_by_fairdata": false,
            "projects": [],
            "provenance": [],
            "relation": [],
            "remote_resources": [],
            "spatial": [],
            "state": "published",
            "temporal": [],
            "theme": [],
            "title": {
                "en": "Computational code underlying the publication “Engineered patterns of Notch ligands Jag1 and Dll4 elicit differential spatial control of endothelial sprouting”"
            },
            "created": "2025-03-17T05:57:23Z",
            "modified": "2025-03-17T05:57:23Z",
            "dataset_versions": [
                {
                    "id": "c93b18b0-3e0b-449c-ba94-59dc05d49e92",
                    "title": {
                        "en": "Computational code underlying the publication “Engineered patterns of Notch ligands Jag1 and Dll4 elicit differential spatial control of endothelial sprouting”"
                    },
                    "persistent_identifier": "doi:10.4121/19235793",
                    "state": "published",
                    "created": "2025-03-17T05:57:23Z",
                    "version": 1
                }
            ],
            "published_revision": 1,
            "version": 1,
            "api_version": 3,
            "metadata_repository": "Fairdata"
        },
        {
            "id": "abc0f726-fefc-4165-8f0c-93851a63dc10",
            "access_rights": {
                "id": "dc93cf1c-3e57-479a-8652-2583721f8de0",
                "license": [
                    {
                        "id": "35b18e72-3819-4ec6-a1be-14624f29d968",
                        "url": "http://uri.suomi.fi/codelist/fairdata/license/code/CC-BY-4.0",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/license",
                        "pref_label": {
                            "en": "Creative Commons Attribution 4.0 International (CC BY 4.0)",
                            "fi": "Creative Commons Nimeä 4.0 Kansainvälinen (CC BY 4.0)"
                        }
                    }
                ],
                "access_type": {
                    "id": "d01ac02c-fc70-4c68-9434-8383cb693ff0",
                    "url": "http://uri.suomi.fi/codelist/fairdata/access_type/code/open",
                    "in_scheme": "http://uri.suomi.fi/codelist/fairdata/access_type",
                    "pref_label": {
                        "en": "Open",
                        "fi": "Avoin"
                    }
                },
                "restriction_grounds": []
            },
            "actors": [
                {
                    "id": "f8c17657-2e09-4692-b69f-5d3ac7faf2ba",
                    "roles": [
                        "contributor"
                    ],
                    "person": {
                        "id": "476b6ace-1b86-4a0d-b474-18ec0cfff30d",
                        "name": "Tiina Salo",
                        "external_identifier": "https://orcid.org/0000-0002-5409-2612"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "d636c3db-fd6a-4dc5-95b8-23503e4788d4",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "f4c6858c-e18f-437d-851b-dd34642f9fe6",
                        "name": "Anniina Nieminen"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "91e02762-bb3a-44b8-b35b-c10b8cbc44ea",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "dc243c2a-db9d-4a8b-830d-1c2d395129b7",
                        "name": "Sonja Salovius-Laurén",
                        "external_identifier": "https://orcid.org/0000-0002-8686-4592"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "07b74ca7-bfb8-477a-a028-c8403e9b17b0",
                    "roles": [
                        "creator"
                    ],
                    "person": {
                        "id": "0f91b592-4b91-43ac-8f72-02d61aac4a51",
                        "name": "Henna Rinne"
                    },
                    "organization": {
                        "id": "a4dc30ef-4be2-412a-a399-ebac8a37213e",
                        "pref_label": {
                            "en": "Åbo Akademi University",
                            "fi": "Åbo Akademi",
                            "sv": "Åbo Akademi",
                            "und": "Åbo Akademi"
                        },
                        "url": "http://uri.suomi.fi/codelist/fairdata/organization/code/01903",
                        "in_scheme": "http://uri.suomi.fi/codelist/fairdata/organization"
                    }
                },
                {
                    "id": "0243434f-086c-4f3e-9df0-201df4dcfb15",
                    "roles": [
                        "publisher"
                    ],
                    "organization": {
                        "id": "8ad6c0d0-47ed-4fba-9620-a9dba829686a",
                        "pref_label": {
                            "en": "Zenodo",
                            "fi": "Zenodo",
                            "sv": "Zenodo"
                        }
                    }
                }
            ],
            "cumulative_state": 0,
            "data_catalog": "urn:nbn:fi:att:data-catalog-abo",
            "description": {
                "en": "Data related to the \"Community science approach reveals temporal and eutrophication-related spatial patterns in bladderwrack-associated invertebrate fauna\" paper by Salo, Nieminen, Salovius-Laurén and Rinne published in Estuarine, Coastal and Shelf Science in 2024. https://doi.org/10.1016/j.ecss.2024.108822 The data describes the community data collected with the community science method described in the paper."
            },
            "field_of_science": [
                {
                    "id": "ea57f07d-16d8-4c7a-8a52-39ef1112278a",
                    "url": "http://www.yso.fi/onto/okm-tieteenala/ta1181",
                    "in_scheme": "http://www.yso.fi/onto/okm-tieteenala/conceptscheme",
                    "pref_label": {
                        "en": "Ecology, evolutionary biology",
                        "fi": "Ekologia, evoluutiobiologia",
                        "sv": "Ekologi, evolutionsbiologi"
                    }
                }
            ],
            "infrastructure": [],
            "issued": "2024-06-05",
            "keyword": [
                "Fucus vesiculosus",
                "education",
                "citizen science",
                "Baltic Sea"
            ],
            "language": [],
            "metadata_owner": {
                "id": "dde6b62a-99e9-49c2-92bc-4a08ae3d9a09",
                "organization": "service_abo"
            },
            "other_identifiers": [],
            "persistent_identifier": "doi:10.5281/zenodo.11482090",
            "pid_generated_by_fairdata": false,
            "projects": [],
            "provenance": [],
            "relation": [],
            "remote_resources": [],
            "spatial": [],
            "state": "published",
            "temporal": [],
            "theme": [],
            "title": {
                "en": "Community science approach reveals temporal and eutrophication-related spatial patterns in bladderwrack-associated invertebrate fauna"
            },
            "created": "2025-03-17T05:57:20Z",
            "modified": "2025-03-17T05:57:20Z",
            "dataset_versions": [
                {
                    "id": "abc0f726-fefc-4165-8f0c-93851a63dc10",
                    "title": {
                        "en": "Community science approach reveals temporal and eutrophication-related spatial patterns in bladderwrack-associated invertebrate fauna"
                    },
                    "persistent_identifier": "doi:10.5281/zenodo.11482090",
                    "state": "published",
                    "created": "2025-03-17T05:57:20Z",
                    "version": 1
                }
            ],
            "published_revision": 1,
            "version": 1,
            "api_version": 3,
            "metadata_repository": "Fairdata"
        }
    ]
}