{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":647381053,"defaultBranch":"main","name":"VisCy","ownerLogin":"mehta-lab","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2023-05-30T16:52:18.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/49008068?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1727486306.0","currentOid":""},"activityList":{"items":[{"before":"4c1b09462c18ce3d30e5239b6edc5419b7f4c06d","after":"3058a8e274d88c93f0fa7061734ac19fde5e4d56","ref":"refs/heads/ram_dataloader","pushedAt":"2024-09-28T18:05:53.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"edyoshikun","name":"Eduardo Hirata-Miyasaki","path":"/edyoshikun","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10470962?s=80&v=4"},"commit":{"message":"adding timeout to ram_dataloader","shortMessageHtmlLink":"adding timeout to ram_dataloader"}},{"before":"b24ff5720ebb136b939960532456df557d19600f","after":"4fe0b926f6d1186a6687a776f3de24a8df6ddd96","ref":"refs/heads/zip-representation","pushedAt":"2024-09-28T14:50:28.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"Soorya19Pradeep","name":null,"path":"/Soorya19Pradeep","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/101817974?s=80&v=4"},"commit":{"message":"add env test detail","shortMessageHtmlLink":"add env test detail"}},{"before":"7b24ea16536cf7022ae896c39e27a12482ad2321","after":"b24ff5720ebb136b939960532456df557d19600f","ref":"refs/heads/zip-representation","pushedAt":"2024-09-28T03:30:24.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ziw-liu","name":"Ziwen Liu","path":"/ziw-liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67518483?s=80&v=4"},"commit":{"message":"bump torch","shortMessageHtmlLink":"bump torch"}},{"before":"85787be9e0e200663625c770e7d33752f57a9d9c","after":null,"ref":"refs/heads/torch241","pushedAt":"2024-09-28T01:18:26.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"edyoshikun","name":"Eduardo Hirata-Miyasaki","path":"/edyoshikun","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10470962?s=80&v=4"}},{"before":"3f580b45e08aa209e1c459c7896d7d5b9ee6ca84","after":"4c1b09462c18ce3d30e5239b6edc5419b7f4c06d","ref":"refs/heads/ram_dataloader","pushedAt":"2024-09-28T01:18:20.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"edyoshikun","name":"Eduardo Hirata-Miyasaki","path":"/edyoshikun","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10470962?s=80&v=4"},"commit":{"message":"Bump torch to 2.4.1 (#174)\n\n* update torch >2.4.1\r\n\r\n* black\r\n\r\n* ruff","shortMessageHtmlLink":"Bump torch to 2.4.1 (#174)"}},{"before":"b2ca7bd2e58e9cdc5c9da0b637ccd2118722e9e7","after":"7b24ea16536cf7022ae896c39e27a12482ad2321","ref":"refs/heads/zip-representation","pushedAt":"2024-09-28T00:52:08.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ziw-liu","name":"Ziwen Liu","path":"/ziw-liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67518483?s=80&v=4"},"commit":{"message":"install in editable mode","shortMessageHtmlLink":"install in editable mode"}},{"before":"8551c8e85ec4c9253d1c2696cbaa3a819327f0ca","after":"b2ca7bd2e58e9cdc5c9da0b637ccd2118722e9e7","ref":"refs/heads/zip-representation","pushedAt":"2024-09-28T00:35:53.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ziw-liu","name":"Ziwen Liu","path":"/ziw-liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67518483?s=80&v=4"},"commit":{"message":"remove dynamic version","shortMessageHtmlLink":"remove dynamic version"}},{"before":"45f3122dfcb51e6afbb385774857222df8cc5b75","after":"8551c8e85ec4c9253d1c2696cbaa3a819327f0ca","ref":"refs/heads/zip-representation","pushedAt":"2024-09-28T00:29:40.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ziw-liu","name":"Ziwen Liu","path":"/ziw-liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67518483?s=80&v=4"},"commit":{"message":"fix config path","shortMessageHtmlLink":"fix config path"}},{"before":"4b036e1446138f374f05c786a2664e1515a1c70e","after":"45f3122dfcb51e6afbb385774857222df8cc5b75","ref":"refs/heads/zip-representation","pushedAt":"2024-09-28T00:28:23.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ziw-liu","name":"Ziwen Liu","path":"/ziw-liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67518483?s=80&v=4"},"commit":{"message":"rename example configs","shortMessageHtmlLink":"rename example configs"}},{"before":"e835e5bcbfe4821f92b45ce460d8aea6ae2eec6b","after":"4b036e1446138f374f05c786a2664e1515a1c70e","ref":"refs/heads/zip-representation","pushedAt":"2024-09-28T00:14:25.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ziw-liu","name":"Ziwen Liu","path":"/ziw-liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67518483?s=80&v=4"},"commit":{"message":"hardcode version","shortMessageHtmlLink":"hardcode version"}},{"before":"d795307a4997c4dd30a519965ebf9506eba3a83d","after":"e835e5bcbfe4821f92b45ce460d8aea6ae2eec6b","ref":"refs/heads/zip-representation","pushedAt":"2024-09-27T23:36:45.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"ziw-liu","name":"Ziwen Liu","path":"/ziw-liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67518483?s=80&v=4"},"commit":{"message":"remove plotting script that needs annotations","shortMessageHtmlLink":"remove plotting script that needs annotations"}},{"before":null,"after":"d795307a4997c4dd30a519965ebf9506eba3a83d","ref":"refs/heads/zip-representation","pushedAt":"2024-09-27T23:31:47.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"ziw-liu","name":"Ziwen Liu","path":"/ziw-liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67518483?s=80&v=4"},"commit":{"message":"remove url","shortMessageHtmlLink":"remove url"}},{"before":"4c48802605ab06ee023c22cb846f86c30d3c1a6d","after":null,"ref":"refs/heads/eval-code","pushedAt":"2024-09-27T21:48:51.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"ziw-liu","name":"Ziwen Liu","path":"/ziw-liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67518483?s=80&v=4"}},{"before":"ad741769183baa4a2313cd4d4c069984a9048735","after":"582952dc0cd4adaf62f07b0b9de009337de26e32","ref":"refs/heads/representation","pushedAt":"2024-09-27T21:48:47.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"ziw-liu","name":"Ziwen Liu","path":"/ziw-liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67518483?s=80&v=4"},"commit":{"message":"updated eval module & cosine sim figures (#168)\n\n* updated files\r\n\r\n* format fixed for tests\r\n\r\n* updated scripts\r\n\r\n* umap dist code\r\n\r\n* bug fixes and linting\r\n\r\n* logistic regression script\r\n\r\n* add infection figure script\r\n\r\n* Add script for generating infection figure and perform prediction on the June dataset\r\n\r\n* Format code\r\n\r\n* Black format evaluation module and fix import in figure_cell_infection script\r\n\r\n* Refactor scatterplot colors and markers\r\n\r\n* Calculate model accuracy\r\n\r\n* Add script for appendix video\r\n\r\n* formatted code\r\n\r\n* updated displacement funcs for full embeddings\r\n\r\n* script for displacement computation\r\n\r\n* fix style\r\n\r\n* fix docstring format\r\n\r\n---------\r\n\r\nCo-authored-by: Shalin Mehta \r\nCo-authored-by: Soorya Pradeep \r\nCo-authored-by: Ziwen Liu ","shortMessageHtmlLink":"updated eval module & cosine sim figures (#168)"}},{"before":"8d6d2df65b02ac249f794e46429a2915bb1f59dd","after":"4c48802605ab06ee023c22cb846f86c30d3c1a6d","ref":"refs/heads/eval-code","pushedAt":"2024-09-27T21:45:45.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"ziw-liu","name":"Ziwen Liu","path":"/ziw-liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67518483?s=80&v=4"},"commit":{"message":"fix docstring format","shortMessageHtmlLink":"fix docstring format"}},{"before":"5dbee3464254c31c3d07d3395e501b41cd728a54","after":"8d6d2df65b02ac249f794e46429a2915bb1f59dd","ref":"refs/heads/eval-code","pushedAt":"2024-09-27T21:43:29.000Z","pushType":"push","commitsCount":13,"pusher":{"login":"ziw-liu","name":"Ziwen Liu","path":"/ziw-liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67518483?s=80&v=4"},"commit":{"message":"Merge branch 'representation' into eval-code","shortMessageHtmlLink":"Merge branch 'representation' into eval-code"}},{"before":"da0bebefcc49d9a2a5294a7a221e6761fbba4826","after":null,"ref":"refs/heads/evaluate_computed_features","pushedAt":"2024-09-27T21:41:30.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"ziw-liu","name":"Ziwen Liu","path":"/ziw-liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67518483?s=80&v=4"}},{"before":"17a2e4828b970ab7fa32cce26bb525c99b7a0292","after":"ad741769183baa4a2313cd4d4c069984a9048735","ref":"refs/heads/representation","pushedAt":"2024-09-27T21:41:27.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"ziw-liu","name":"Ziwen Liu","path":"/ziw-liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67518483?s=80&v=4"},"commit":{"message":"Fixes on correlation of PCA and UMAP components to computed_feature script (#159)\n\n* reduce initial patch size\r\n\r\n* add radial profiling\r\n\r\n* add function descriptions\r\n\r\n* add umap correlation\r\n\r\n* add def comments\r\n\r\n* change umap for all data\r\n\r\n* add script for 1 chan\r\n\r\n* add p-value analysis\r\n\r\n* add PCA analysis\r\n\r\n* remove duplicate script\r\n\r\n* Refactor and format code\r\n\r\n* Format code\r\n\r\n* Removed umap correlation\r\n\r\n* note for future refactor\r\n\r\n---------\r\n\r\nCo-authored-by: Ziwen Liu ","shortMessageHtmlLink":"Fixes on correlation of PCA and UMAP components to computed_feature s…"}},{"before":"f7160c9d6ca4dc8942aa01020ef2ca7c863ec820","after":"da0bebefcc49d9a2a5294a7a221e6761fbba4826","ref":"refs/heads/evaluate_computed_features","pushedAt":"2024-09-27T21:40:38.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ziw-liu","name":"Ziwen Liu","path":"/ziw-liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67518483?s=80&v=4"},"commit":{"message":"note for future refactor","shortMessageHtmlLink":"note for future refactor"}},{"before":"3e215b559746480de9dd4c7ea811cfaeb84aa2fa","after":"f7160c9d6ca4dc8942aa01020ef2ca7c863ec820","ref":"refs/heads/evaluate_computed_features","pushedAt":"2024-09-27T21:39:09.000Z","pushType":"push","commitsCount":20,"pusher":{"login":"ziw-liu","name":"Ziwen Liu","path":"/ziw-liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67518483?s=80&v=4"},"commit":{"message":"Merge branch 'representation' into evaluate_computed_features","shortMessageHtmlLink":"Merge branch 'representation' into evaluate_computed_features"}},{"before":"df9a5cd086dad1f061326a1b0cc0b2f3a861f0ea","after":"17a2e4828b970ab7fa32cce26bb525c99b7a0292","ref":"refs/heads/representation","pushedAt":"2024-09-27T20:25:32.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"Soorya19Pradeep","name":null,"path":"/Soorya19Pradeep","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/101817974?s=80&v=4"},"commit":{"message":"remove reduntant script","shortMessageHtmlLink":"remove reduntant script"}},{"before":"42a0cb5755e61d39b4cc175043a93a548d0f0725","after":"df9a5cd086dad1f061326a1b0cc0b2f3a861f0ea","ref":"refs/heads/representation","pushedAt":"2024-09-27T20:24:12.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"Soorya19Pradeep","name":null,"path":"/Soorya19Pradeep","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/101817974?s=80&v=4"},"commit":{"message":"reduce to single arrow on plot","shortMessageHtmlLink":"reduce to single arrow on plot"}},{"before":"7e66c3d526542cc5b02fef7ca03377ca47be35b5","after":null,"ref":"refs/heads/hf_badge","pushedAt":"2024-09-27T20:19:52.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"ziw-liu","name":"Ziwen Liu","path":"/ziw-liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67518483?s=80&v=4"}},{"before":"f3ac68094922f6c741f20a2f6ad530b6befe64e7","after":"a0dcbde3b12c18b01708d9df3a0941103903bd8b","ref":"refs/heads/main","pushedAt":"2024-09-27T20:19:49.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"ziw-liu","name":"Ziwen Liu","path":"/ziw-liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67518483?s=80&v=4"},"commit":{"message":"adding VS hugginface demo (#172)\n\n* demo vs hugginface\r\n\r\n* clicking gif points to hf space\r\n\r\n* center gif\r\n\r\n* fixing links\r\n\r\n* centering gif\r\n\r\n* break line for badge\r\n\r\n* absolute path for gif\r\n\r\n* center gif in readme (#175)\r\n\r\n---------\r\n\r\nCo-authored-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>","shortMessageHtmlLink":"adding VS hugginface demo (#172)"}},{"before":"58b9fea2b312ffabbc2fd8cb72f3606720dfbb10","after":null,"ref":"refs/heads/bridge-gaps","pushedAt":"2024-09-27T18:35:36.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"ziw-liu","name":"Ziwen Liu","path":"/ziw-liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67518483?s=80&v=4"}},{"before":"10219d348bd4ec5f061f8899be83ede1502d150f","after":"42a0cb5755e61d39b4cc175043a93a548d0f0725","ref":"refs/heads/representation","pushedAt":"2024-09-27T18:35:33.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"ziw-liu","name":"Ziwen Liu","path":"/ziw-liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67518483?s=80&v=4"},"commit":{"message":"UMAP line plot to assess temporal smoothness in features space (#176)\n\n* add maplotlib style sheet for figure making\r\n\r\n* add cell division attribution\r\n\r\n* add matplotlib style sheet\r\n\r\n* move attribution computation to lca\r\n\r\n* tweak contrast limits and text\r\n\r\n* add captum to optional dependencies\r\n\r\n* move attribution function to a method of the classifier\r\n\r\n* add script to show organelle dynamics\r\n\r\n* add occlusion attribution\r\n\r\n* more generic save path\r\n\r\n* add uninfected cell\r\n\r\n* tweak subplot spacing\r\n\r\n* lower case titles\r\n\r\n* reduce UMAP components to 2 and add indices\r\n\r\n* add script to make the bridge gaps figure","shortMessageHtmlLink":"UMAP line plot to assess temporal smoothness in features space (#176)"}},{"before":"6ed3e64d3ce384df388d59cb63c062dfeb5f484e","after":"58b9fea2b312ffabbc2fd8cb72f3606720dfbb10","ref":"refs/heads/bridge-gaps","pushedAt":"2024-09-27T16:53:56.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"ziw-liu","name":"Ziwen Liu","path":"/ziw-liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67518483?s=80&v=4"},"commit":{"message":"Merge branch 'representation' into bridge-gaps","shortMessageHtmlLink":"Merge branch 'representation' into bridge-gaps"}},{"before":null,"after":"6ed3e64d3ce384df388d59cb63c062dfeb5f484e","ref":"refs/heads/bridge-gaps","pushedAt":"2024-09-27T16:48:23.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"ziw-liu","name":"Ziwen Liu","path":"/ziw-liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67518483?s=80&v=4"},"commit":{"message":"add script to make the bridge gaps figure","shortMessageHtmlLink":"add script to make the bridge gaps figure"}},{"before":"bf1c4fcf1a474a98611ecbde045c107a72657079","after":"85787be9e0e200663625c770e7d33752f57a9d9c","ref":"refs/heads/torch241","pushedAt":"2024-09-27T04:14:37.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"edyoshikun","name":"Eduardo Hirata-Miyasaki","path":"/edyoshikun","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10470962?s=80&v=4"},"commit":{"message":"ruff","shortMessageHtmlLink":"ruff"}},{"before":"1c00057a6d02ee0dcda15d755bc00484e938f2d6","after":"3f580b45e08aa209e1c459c7896d7d5b9ee6ca84","ref":"refs/heads/ram_dataloader","pushedAt":"2024-09-27T04:13:30.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"edyoshikun","name":"Eduardo Hirata-Miyasaki","path":"/edyoshikun","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10470962?s=80&v=4"},"commit":{"message":"ruff","shortMessageHtmlLink":"ruff"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"startCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOS0yOFQxODowNTo1My4wMDAwMDBazwAAAATDeyt1","endCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOS0yN1QwNDoxMzozMC4wMDAwMDBazwAAAATCLjGo"}},"title":"Activity · mehta-lab/VisCy"}