{ "created": "2024-06-14T13:49:38.435685+00:00", "modified": "2024-06-14T13:49:38.839835+00:00", "id": 11657620, "conceptrecid": "10636590", "doi": "10.5281/zenodo.11657620", "conceptdoi": "10.5281/zenodo.10636590", "doi_url": "https://doi.org/10.5281/zenodo.11657620", "metadata": { "title": "HoVer-NeXt: A Fast Nuclei Segmentation and Classification Pipeline for Next Generation Histopathology - Datasets", "doi": "10.5281/zenodo.11657620", "publication_date": "2024-06-14", "description": "

This repository contains training and validation data for

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HoVer-NeXt: A Fast Nuclei Segmentation and Classification Pipeline for Next Generation Histopathology 

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Accepted for Oral Presentation at MIDL2024: https://openreview.net/pdf?id=3vmB43oqIO 

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More information and code are available at https://github.com/digitalpathologybern/hover_next_inference

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Modified Lizard dataset to include mitosis (lizard_mitosis.zip), mitosis dataset (mitosis_ds.zip) and a holdout eosinophil validation set (eos_eval.zip)

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mitosis_ds.zip also contains the hold-out H&E mitosis test set.

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The original lizard dataset was createdy by Simon Graham et al. and was shared under CC BY-NC-SA 4.0. The tile-based dataset can be downloaded from https://conic-challenge.grand-challenge.org/Data/ after registering for the challenge. We modify the dataset by including an additional mitosis class, however note that there are a number of mitosis which are still not (correctly annotated).

", "access_right": "open", "creators": [ { "name": "Baumann, Elias", "affiliation": "University of Bern", "orcid": "0000-0003-4655-4925" }, { "name": "Dislich, Bastian", "affiliation": "University of Bern", "orcid": "0000-0002-4838-4686" }, { "name": "Rumberger, Josef Lorenz", "affiliation": "Max Delbr\u00fcck Center", "orcid": "0000-0002-7225-7011" }, { "name": "Nagtegaal, Iris D.", "affiliation": "Radboud University Medical Center", "orcid": "0000-0003-0887-4127" }, { "name": "Mart\u00ednez Rodr\u00edguez, Mar\u00eda", "affiliation": "Yale School of Medicine" }, { "name": "Zlobec, Inti", "affiliation": "University of Bern", "orcid": "0000-0001-6741-3000" } ], "references": [ "Graham, S., Jahanifar, M., Azam, A.S., Nimir, M., Tsang, Y., Dodd, K.C., Hero, E., Sahota, H., Tank, A., Benes, K., Wahab, N., Minhas, F.A., Raza, S.E., Eldaly, H., Gopalakrishnan, K., Snead, D.R., & Rajpoot, N.M. (2021). Lizard: A Large-Scale Dataset for Colonic Nuclear Instance Segmentation and Classification. 2021 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW), 684-693." ], "custom": { "code:programmingLanguage": [ { "id": "python", "title": { "en": "Python" } } ], "code:developmentStatus": { "id": "active", "title": { "en": "Active" } } }, "resource_type": { "title": "Dataset", "type": "dataset" }, "license": { "id": "cc-by-nc-sa-4.0" }, "relations": { "version": [ { "index": 1, "is_last": true, "parent": { "pid_type": "recid", "pid_value": "10636590" } } ] } }, "title": "HoVer-NeXt: A Fast Nuclei Segmentation and Classification Pipeline for Next Generation Histopathology - Datasets", "links": { "self": "https://zenodo.org/api/records/11657620", "self_html": "https://zenodo.org/records/11657620", "preview_html": "https://zenodo.org/records/11657620?preview=1", "doi": "https://doi.org/10.5281/zenodo.11657620", "self_doi": "https://doi.org/10.5281/zenodo.11657620", "self_doi_html": "https://zenodo.org/doi/10.5281/zenodo.11657620", "reserve_doi": "https://zenodo.org/api/records/11657620/draft/pids/doi", "parent": "https://zenodo.org/api/records/10636590", "parent_html": "https://zenodo.org/records/10636590", "parent_doi": "https://doi.org/10.5281/zenodo.10636590", "parent_doi_html": "https://zenodo.org/doi/10.5281/zenodo.10636590", "self_iiif_manifest": "https://zenodo.org/api/iiif/record:11657620/manifest", "self_iiif_sequence": "https://zenodo.org/api/iiif/record:11657620/sequence/default", "files": "https://zenodo.org/api/records/11657620/files", "media_files": "https://zenodo.org/api/records/11657620/media-files", "latest": "https://zenodo.org/api/records/11657620/versions/latest", "latest_html": "https://zenodo.org/records/11657620/latest", "versions": "https://zenodo.org/api/records/11657620/versions", "draft": "https://zenodo.org/api/records/11657620/draft", "access_links": "https://zenodo.org/api/records/11657620/access/links", "access_grants": "https://zenodo.org/api/records/11657620/access/grants", "access_users": "https://zenodo.org/api/records/11657620/access/users", "access_request": "https://zenodo.org/api/records/11657620/access/request", "access": "https://zenodo.org/api/records/11657620/access", "communities": "https://zenodo.org/api/records/11657620/communities", "communities-suggestions": "https://zenodo.org/api/records/11657620/communities-suggestions", "request_deletion": "https://zenodo.org/api/records/11657620/request-deletion", "file_modification": "https://zenodo.org/api/records/11657620/file-modification", "quota_increase": "https://zenodo.org/api/records/11657620/quota-increase", "requests": "https://zenodo.org/api/records/11657620/requests" }, "updated": "2024-06-14T13:49:38.839835+00:00", "recid": "11657620", "revision": 4, "files": [ { "id": "d3ed4173-88df-44cb-974b-a5679d0850a5", "key": "mitosis_ds.zip", "size": 941412724, "checksum": "md5:97575c31909b8121074d1eb03430104c", "links": { "self": "https://zenodo.org/api/records/11657620/files/mitosis_ds.zip/content" } }, { "id": "d601e514-48b2-490b-ac83-45b1d2dde829", "key": "lizard_mitosis.zip", "size": 888717653, "checksum": "md5:126951a466de9b84b12ad89f3adc81e6", "links": { "self": "https://zenodo.org/api/records/11657620/files/lizard_mitosis.zip/content" } }, { "id": "735c23c0-ec10-46f3-961d-468da9b56da3", "key": "eos_val.zip", "size": 899625086, "checksum": "md5:3099e0e0dc6c509d6c42c22188c51d3a", "links": { "self": "https://zenodo.org/api/records/11657620/files/eos_val.zip/content" } }, { "id": "2cc2eed0-1bbd-41db-8fb5-8b92a03a5165", "key": "mit_val.zip", "size": 562588042, "checksum": "md5:cac6d0c7c35972cc0889eb3dd30d5708", "links": { "self": "https://zenodo.org/api/records/11657620/files/mit_val.zip/content" } } ], "swh": {}, "owners": [ { "id": "313467" } ], "status": "published", "stats": { "downloads": 1346, "unique_downloads": 1023, "views": 1361, "unique_views": 1306, "version_downloads": 618, "version_unique_downloads": 530, "version_unique_views": 712, "version_views": 748 }, "state": "done", "submitted": true }