{"id":16770507,"url":"https://github.com/cxhernandez/cellcount","last_synced_at":"2025-03-21T23:34:06.500Z","repository":{"id":67233854,"uuid":"91720340","full_name":"cxhernandez/cellcount","owner":"cxhernandez","description":"A Convolutional Neural Network for Segmenting and Counting Cells in Microscopy Images","archived":false,"fork":false,"pushed_at":"2019-04-16T14:50:36.000Z","size":4262,"stargazers_count":58,"open_issues_count":1,"forks_count":23,"subscribers_count":8,"default_branch":"master","last_synced_at":"2025-03-18T06:11:42.940Z","etag":null,"topics":["biology","computer-vision","python","pytorch","segmentation"],"latest_commit_sha":null,"homepage":"","language":"TeX","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cxhernandez.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2017-05-18T17:27:29.000Z","updated_at":"2024-08-04T00:52:16.000Z","dependencies_parsed_at":null,"dependency_job_id":"90e340bd-6413-4a56-bac7-658c11d746ca","html_url":"https://github.com/cxhernandez/cellcount","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cxhernandez%2Fcellcount","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cxhernandez%2Fcellcount/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cxhernandez%2Fcellcount/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cxhernandez%2Fcellcount/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cxhernandez","download_url":"https://codeload.github.com/cxhernandez/cellcount/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244885400,"owners_count":20526291,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["biology","computer-vision","python","pytorch","segmentation"],"created_at":"2024-10-13T06:24:29.887Z","updated_at":"2025-03-21T23:34:06.083Z","avatar_url":"https://github.com/cxhernandez.png","language":"TeX","funding_links":[],"categories":[],"sub_categories":[],"readme":"# cellcount\n\nThis is a Python 3.4+ project that uses PyTorch v0.4.1.\n\n## Example Usage\n\nAfter installing via `python setup.py install`, you can use the command-line commands to download an example BBBC dataset, train the feature pyramid network (FPN), and finally train the fulll end-to-end cell counting network:\n\n```\n$ cell_count download --dataset bbbc005\n$ cell_count train_fpn --dataset path/to/bbbc005\n$ cell_count train --dataset path/to/bbbc005\n```\n\n## Citing\n\nIf you find this software useful for your work, please cite:\n\n```bibtex\n@article{cellcount,\nAuthor = {Carlos X. Hernández and Mohammad M. Sultan and Vijay S. Pande},\nTitle = {Using Deep Learning for Segmentation and Counting within Microscopy Data},\nYear = {2018},\nEprint = {arXiv:1802.10548},\n}\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcxhernandez%2Fcellcount","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcxhernandez%2Fcellcount","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcxhernandez%2Fcellcount/lists"}