Team Ai
Datasetpublic

OpenScientificCodeRegistry/Database

Open Scientific Code Registry (OSCR): the authors' scripts The code published by the authors of open-access neuroscience papers, as found and verified by Open Scientific Code Registry (OSCR). Each file is here exactly as it is at the source, at the verified commit, under the license of its repository. 421,275 unique files (3,782 MB of text) from 8,849 repositories, in 24 Parquet block(s). Only files whose repository's license allows redistribution, confirmed by the repository's… See the full description on the dataset page: https://huggingface.co/datasets/OpenScientificCodeRegistry/Database.

sourceHugging Faceotherupdated 2d agoView on Hugging Face
0likes5.6kdownloads
github.com__map-science__deepaxonmyelinemsegmenter.json480 linesDownload Raw Back to a2
1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/map-science/deepaxonmyelinemsegmenter",4 "url": "https://github.com/MaP-science/DeepAxonMyelinEMSegmenter/tree/skoven-c-2025",5 "host": "github.com",6 "commit": "faa0a772379cc4bf8c20b09a19db72696474f727",7 "license": "Apache-2.0",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11  {12   "path": "LICENSE",13   "sha256": "c71d239df91726fc519c6eb72d318ec65820627232b2f796219e87dcf35d0ab4",14   "language": "License",15   "lines": 201,16   "truncated": false,17   "block": 1,18   "row": 221619  },20  {21   "path": "README.md",22   "sha256": "53380b87947cb10cf988089040c5d2322da310661557e495e20c0022cefb75b4",23   "language": "Text",24   "lines": 111,25   "truncated": false,26   "block": 16,27   "row": 735328  },29  {30   "path": "SkovenC_analysis/90percentile.ipynb",31   "sha256": "c59b1b8c2fb2318f5f226c5db1956a858acc116955e029c389a019cd4bf017cd",32   "language": "Jupyter",33   "lines": 534,34   "truncated": false,35   "block": 14,36   "row": 1636237  },38  {39   "path": "SkovenC_analysis/90percentile_loc0.ipynb",40   "sha256": "d2b61d060a54b37b3d2b7c4a1c1a38a02d7ee1a20a7cfde35e19ccaa42b28b51",41   "language": "Jupyter",42   "lines": 528,43   "truncated": false,44   "block": 14,45   "row": 1635546  },47  {48   "path": "SkovenC_analysis/per_sample.ipynb",49   "sha256": "bb27ca1a69f22f6f10418919bbe083e87278913508f0b05d8d4a35e8c695b2a4",50   "language": "Jupyter",51   "lines": 43,52   "truncated": false,53   "block": 14,54   "row": 1489255  },56  {57   "path": "SkovenC_analysis/refined_metrics_plots.ipynb",58   "sha256": "8a4c442985f6f3857aa67dc0c711e5bbe81c9415183f6795cf125ee8a0d437ee",59   "language": "Jupyter",60   "lines": 55,61   "truncated": false,62   "block": 14,63   "row": 1496464  },65  {66   "path": "archive/downsampling.ipynb",67   "sha256": "6896464c7d459e12e2ca14882c6f9b539a11dde6bea1b6ffb1def27f2101a317",68   "language": "Jupyter",69   "lines": 78,70   "truncated": false,71   "block": 14,72   "row": 1503073  },74  {75   "path": "archive/models/unet3d_0.py",76   "sha256": "9879e7ad362c6f471312644774522329bb1136a971a2d84a4a63a4e9901f8eac",77   "language": "Python",78   "lines": 127,79   "truncated": false,80   "block": 15,81   "row": 1723782  },83  {84   "path": "archive/models/unet3d_0_binary.py",85   "sha256": "b996ced0a2ffd966db6e4e394a8f73c73872a1cf87d23287816a78b8d84a04fc",86   "language": "Python",87   "lines": 131,88   "truncated": false,89   "block": 15,90   "row": 1751591  },92  {93   "path": "archive/models/unet3d_0_k5.py",94   "sha256": "d2572e2cc2a1983c39c38a654484289f0f4439701d508bcdb28860ca101424ff",95   "language": "Python",96   "lines": 127,97   "truncated": false,98   "block": 15,99   "row": 17224100  },101  {102   "path": "archive/process_annotations.ipynb",103   "sha256": "b21bc9d108b2a456e3a4403f8ec0334bf0dceb82fa1ad71cd98500ce9269233b",104   "language": "Jupyter",105   "lines": 250,106   "truncated": false,107   "block": 14,108   "row": 15881109  },110  {111   "path": "archive/process_manual_annotations.ipynb",112   "sha256": "a288e852824a6c2a83b8eabe617103acf2446b258ef86e090499c293db99f722",113   "language": "Jupyter",114   "lines": 230,115   "truncated": false,116   "block": 14,117   "row": 15839118  },119  {120   "path": "config.py",121   "sha256": "b7b6ef2b6b44dce86109dcdb02901c57f3fa1daf785c97b6f39fb4480831235a",122   "language": "Python",123   "lines": 103,124   "truncated": false,125   "block": 15,126   "row": 15225127  },128  {129   "path": "config_pred.py",130   "sha256": "d76a8c31e819c596c94eaf22d536fe9377ba752ae54d9927c65d5f63793b25db",131   "language": "Python",132   "lines": 98,133   "truncated": false,134   "block": 15,135   "row": 14745136  },137  {138   "path": "jobfile_gpu.sh",139   "sha256": "8a275aa9c06b62bfc799466ca5875784dc129ec211d4de482277aa6b4e742544",140   "language": "Shell",141   "lines": 63,142   "truncated": false,143   "block": 16,144   "row": 6202145  },146  {147   "path": "jobfile_gpu_pred.sh",148   "sha256": "3931c7a4d7a315090faf30d41c402486522dc9c87429b53a2012c7553abbc781",149   "language": "Shell",150   "lines": 64,151   "truncated": false,152   "block": 16,153   "row": 6206154  },155  {156   "path": "jobfile_hpc.sh",157   "sha256": "724910d2d204fa3ba1368d508163f08ea42e999cc98fb4b82d6ca63b0c76899a",158   "language": "Shell",159   "lines": 54,160   "truncated": false,161   "block": 16,162   "row": 6209163  },164  {165   "path": "main.py",166   "sha256": "868e41fdbc15c20c55bec333eb02687b20a7bc56521edcc81cff0a74cb5bd6a0",167   "language": "Python",168   "lines": 576,169   "truncated": false,170   "block": 16,171   "row": 266172  },173  {174   "path": "models/unet3d.py",175   "sha256": "c206209d93f4b4e8e7601fc62ef2b68e3264a303431eba024a1c1469959ac532",176   "language": "Python",177   "lines": 171,178   "truncated": false,179   "block": 15,180   "row": 19251181  },182  {183   "path": "postprocessing/Axon_Diam_&_GRatio.ipynb",184   "sha256": "d4e729e9acb57a8e3b259486aacaf717fa4bd62b5c3ea650b58f8f097c714718",185   "language": "Jupyter",186   "lines": 298,187   "truncated": false,188   "block": 14,189   "row": 16041190  },191  {192   "path": "postprocessing/DismissManualAnnotations.ipynb",193   "sha256": "a42d7dbd2c8e368f68d86c38bfbcaccae59cb5f8051e15a7b0b2c209d6fde929",194   "language": "Jupyter",195   "lines": 92,196   "truncated": false,197   "block": 14,198   "row": 15229199  },200  {201   "path": "postprocessing/DismissManualAnnotations15.5.ipynb",202   "sha256": "781764891799b2cb4462abd86245ce45adf3163eed8734c0a05fff3dd2485446",203   "language": "Jupyter",204   "lines": 89,205   "truncated": false,206   "block": 14,207   "row": 15244208  },209  {210   "path": "postprocessing/fibers_seg.ipynb",211   "sha256": "8006771807363f40a6464d3234599d2377612132268962a49941811445832dd8",212   "language": "Jupyter",213   "lines": 191,214   "truncated": false,215   "block": 14,216   "row": 15446217  },218  {219   "path": "postprocessing/fibers_viz.ipynb",220   "sha256": "dcd0941479fbd9bca9a80d9744b1b37f97d4c98fa33281cd20f3a349acc78162",221   "language": "Jupyter",222   "lines": 113,223   "truncated": false,224   "block": 14,225   "row": 14991226  },227  {228   "path": "postprocessing/spokes.ipynb",229   "sha256": "52b46c262c5abc921ac78a0c85ab0d13369408f3dddd8f9c2aa80345c8038749",230   "language": "Jupyter",231   "lines": 273,232   "truncated": false,233   "block": 14,234   "row": 15902235  },236  {237   "path": "predict_all.py",238   "sha256": "63df8c50f3cf135e1c9077f1ba3e5e47776185eee35b52cfc1347ff9708fab1c",239   "language": "Python",240   "lines": 309,241   "truncated": false,242   "block": 15,243   "row": 23668244  },245  {246   "path": "preprocessing/preprocess_for_model.ipynb",247   "sha256": "2b764291b3a7be1741a91178e9ea969a299f7a12eaae009c9ecf2d4e9f200d7d",248   "language": "Jupyter",249   "lines": 165,250   "truncated": false,251   "block": 14,252   "row": 15515253  },254  {255   "path": "preprocessing/raw_data_metadata_cryo.ipynb",256   "sha256": "6b25d67522cbee215466f44c206c7e9d5506cd135bc8a58f4277329428c1368f",257   "language": "Jupyter",258   "lines": 145,259   "truncated": false,260   "block": 14,261   "row": 15542262  },263  {264   "path": "preprocessing/raw_data_metadata_epon.ipynb",265   "sha256": "20fd904adcf2039948fdb10fd0df507c50d9b4302246102b96df553decf3c5a9",266   "language": "Jupyter",267   "lines": 145,268   "truncated": false,269   "block": 14,270   "row": 15539271  },272  {273   "path": "run_clean_ADS_seg.sh",274   "sha256": "680cb7164b7081feab8595a79c948ef8c3acfbde21777917ec950cb12f9bf6b6",275   "language": "Shell",276   "lines": 14,277   "truncated": false,278   "block": 16,279   "row": 4881280  },281  {282   "path": "submit_job_gpu.sh",283   "sha256": "97cb8a1c48b5e00fccb50202c3e1698afaddd2f4bdd0c1df0609bf38662a1baa",284   "language": "Shell",285   "lines": 26,286   "truncated": false,287   "block": 16,288   "row": 5339289  },290  {291   "path": "submit_job_gpu_pred.sh",292   "sha256": "0d8eaa6c808efd7f6116355d37003da9cc45277529ef43119ed96ec1d8f2a57f",293   "language": "Shell",294   "lines": 26,295   "truncated": false,296   "block": 16,297   "row": 5347298  },299  {300   "path": "submit_job_hpc.sh",301   "sha256": "7aa0336d4c86faaaea9c755918737c34b66ba71d2b5ba1eeecef09962cfd0855",302   "language": "Shell",303   "lines": 26,304   "truncated": false,305   "block": 16,306   "row": 5338307  },308  {309   "path": "submit_run_clean_ADS_seg.sh",310   "sha256": "9390954bd7d291c9701f4eedab4f3ba200128b11cc8532467d8e2087720ee2b7",311   "language": "Shell",312   "lines": 26,313   "truncated": false,314   "block": 16,315   "row": 5237316  },317  {318   "path": "utils/CELoss.py",319   "sha256": "8a1d5ad68ba1a1cbfbd3f668c552f8d6d04d67583df76161e24f41a4fd1b7508",320   "language": "Python",321   "lines": 99,322   "truncated": false,323   "block": 15,324   "row": 14329325  },326  {327   "path": "utils/CustomGridSampler.py",328   "sha256": "e2119469313a89d76cea12e17faeaeebd64236045dfa851d446e37019cbe3c5a",329   "language": "Python",330   "lines": 212,331   "truncated": false,332   "block": 15,333   "row": 21322334  },335  {336   "path": "utils/CustomGridSamplerNoAug.py",337   "sha256": "dae0300b9a0137569b05076d32ab6f64e437cdf10dccf07c6eb5a8205d6d8a4f",338   "language": "Python",339   "lines": 217,340   "truncated": false,341   "block": 15,342   "row": 21482343  },344  {345   "path": "utils/MaskedDiceCELoss.py",346   "sha256": "5d982c4898b7c08f442623e3caaa1c4b1b5840d0ebc9c21f9b8aac16245266d4",347   "language": "Python",348   "lines": 162,349   "truncated": false,350   "block": 15,351   "row": 20045352  },353  {354   "path": "utils/MaskedGeneralizedDiceCELoss.py",355   "sha256": "cf290d52dcd723928e810f9027850987e370e7508890b7af18b40f2da0359c8c",356   "language": "Python",357   "lines": 161,358   "truncated": false,359   "block": 15,360   "row": 20039361  },362  {363   "path": "utils/MaskedGeneralizedDiceLoss.py",364   "sha256": "8559fac00c9fc8680fd4c7722cf4f7288375b2a5d5475f07a2b358ec27af24e3",365   "language": "Python",366   "lines": 54,367   "truncated": false,368   "block": 15,369   "row": 11253370  },371  {372   "path": "utils/aux.ipynb",373   "sha256": "a9ed13451d83e7dded356fc3bcc4e08cc99d55e1cfe6b6179d6480820b53ba16",374   "language": "Jupyter",375   "lines": 118,376   "truncated": false,377   "block": 14,378   "row": 15184379  },380  {381   "path": "utils/blob_analysis.py",382   "sha256": "cf9163fc0a6897c1341d2328820ce59369b4a38b339098b54c212e1a1e9ddc8a",383   "language": "Python",384   "lines": 250,385   "truncated": false,386   "block": 15,387   "row": 22997388  },389  {390   "path": "utils/clean_ADS_seg.py",391   "sha256": "351a5a1b71a48da60aba02f09045c17b0133861efac8df1d18463f8a91b85f8f",392   "language": "Python",393   "lines": 273,394   "truncated": false,395   "block": 15,396   "row": 22949397  },398  {399   "path": "utils/clean_ADS_seg_15.5.py",400   "sha256": "064163cd627b010c4e3dfaf06501636c0eeef47d7101ef72f924c83e800f7ad7",401   "language": "Python",402   "lines": 183,403   "truncated": false,404   "block": 15,405   "row": 20543406  },407  {408   "path": "utils/parallel_funcs.py",409   "sha256": "60d8ec57a98106a08bef9b7bab74a71dca158ce243f95371d6a8cc1df036808d",410   "language": "Python",411   "lines": 172,412   "truncated": false,413   "block": 15,414   "row": 20093415  },416  {417   "path": "utils/per_sample.ipynb",418   "sha256": "c96e58dbca5818c0219be1519f925962de892796c77a87837ad7d86270287516",419   "language": "Jupyter",420   "lines": 48,421   "truncated": false,422   "block": 14,423   "row": 15043424  },425  {426   "path": "utils/preprocess.py",427   "sha256": "ebd110b13a05514657be9a7dfa48f2c5488f0adb2dbb5215f4b83030011abdfb",428   "language": "Python",429   "lines": 148,430   "truncated": false,431   "block": 15,432   "row": 18299433  },434  {435   "path": "utils/pytorchtools.py",436   "sha256": "adaa890cf8bb7fba9f646b80454eabf72b9a508752096bbb2b2c6ba63855925d",437   "language": "Python",438   "lines": 79,439   "truncated": false,440   "block": 15,441   "row": 14024442  },443  {444   "path": "utils/reorient.ipynb",445   "sha256": "b18c910503f0577038b871a9ddd108d421d5395a71ede8109763deda5f6a6e89",446   "language": "Jupyter",447   "lines": 33,448   "truncated": false,449   "block": 14,450   "row": 14807451  },452  {453   "path": "utils/spokes.py",454   "sha256": "a98a6d999d81d9d51516c9c7d15c988270b8cb1c6a21734443ad0510ae511701",455   "language": "Python",456   "lines": 152,457   "truncated": false,458   "block": 15,459   "row": 18301460  },461  {462   "path": "utils/to_nii_gz.ipynb",463   "sha256": "9aad14411579106b81fcc0454ef203f55a5c0ddc10d5d1f49a5d8eff1e65e85d",464   "language": "Jupyter",465   "lines": 149,466   "truncated": false,467   "block": 14,468   "row": 15328469  },470  {471   "path": "utils/utils.py",472   "sha256": "e3e62b9ecb99961653634d24b3020e95e404c8280207a87ac423d5d0787e5824",473   "language": "Python",474   "lines": 202,475   "truncated": false,476   "block": 15,477   "row": 21152478  }479 ]480}