OpenScientificCodeRegistry/Database

1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/schnitzer-lab/extract-public",4 "url": "https://github.com/schnitzer-lab/EXTRACT-public",5 "host": "github.com",6 "commit": "2c7495700d2a88c1daa2a69652fd3abaa4b261a7",7 "license": "MIT",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11  {12   "path": "EXTRACT/get_defaults.m",13   "sha256": "5802136fc8ddda1fcc7963189ab7e2b48cb661a0bf20ade5c6df8cca4e3c9918",14   "language": "MATLAB",15   "lines": 193,16   "truncated": false,17   "block": 22,18   "row": 2390919  },20  {21   "path": "EXTRACT/main_functions/debug_utils/brewermap/brewermap.m",22   "sha256": "d114912cc8ec123d0d57b9bc82821c17c5a5d0c6f8a449f7060bf02e8a6d5613",23   "language": "MATLAB",24   "lines": 528,25   "truncated": false,26   "block": 22,27   "row": 2466228  },29  {30   "path": "EXTRACT/main_functions/debug_utils/brewermap/brewermap_view.m",31   "sha256": "b3e5e348462bd10ff4c1a1b13be4c8fc2c21e5b587e151734a659a9a28475457",32   "language": "MATLAB",33   "lines": 345,34   "truncated": false,35   "block": 22,36   "row": 2389637  },38  {39   "path": "EXTRACT/main_functions/debug_utils/classification_hyperparameters.m",40   "sha256": "7cec120f3e3551918dcb04a880ac1f42ac856479f44ce68916d330d478772b31",41   "language": "MATLAB",42   "lines": 66,43   "truncated": false,44   "block": 22,45   "row": 2042546  },47  {48   "path": "EXTRACT/main_functions/debug_utils/combine_all_traces_and_images.m",49   "sha256": "f07a2c5123e7e9e7e1f1ae09d19de77181a00105f935c27d4d102b659f7d604a",50   "language": "MATLAB",51   "lines": 10,52   "truncated": false,53   "block": 22,54   "row": 1475855  },56  {57   "path": "EXTRACT/main_functions/debug_utils/detect_ca_events.m",58   "sha256": "08330c6ac879079e4bf6f75d6971c67387fa793b7373996c6ac451dfd80a3150",59   "language": "MATLAB",60   "lines": 68,61   "truncated": false,62   "block": 22,63   "row": 1939664  },65  {66   "path": "EXTRACT/main_functions/debug_utils/get_S_surround.m",67   "sha256": "a9159ac07a1fb1f1c7d9fb03d64e1db61c7f581151585d97462d1924cff8a881",68   "language": "MATLAB",69   "lines": 17,70   "truncated": false,71   "block": 22,72   "row": 1548373  },74  {75   "path": "EXTRACT/main_functions/debug_utils/get_T_ls.m",76   "sha256": "405135b7d0c3da8b27085712e7f18fd9cfc485dc979e58c892e38b98dea5b3f0",77   "language": "MATLAB",78   "lines": 10,79   "truncated": false,80   "block": 22,81   "row": 1483482  },83  {84   "path": "EXTRACT/main_functions/debug_utils/get_bad_cell_stats.m",85   "sha256": "381a7b6d6749a67f56b8be42c4234257899d53517351ae222128edd479240a72",86   "language": "MATLAB",87   "lines": 24,88   "truncated": false,89   "block": 22,90   "row": 1663791  },92  {93   "path": "EXTRACT/main_functions/debug_utils/get_bad_images_and_traces.m",94   "sha256": "e336f31f566e817d7dbebe0f3d7c508f6ae0829e9b468228974f01fcf395cf78",95   "language": "MATLAB",96   "lines": 28,97   "truncated": false,98   "block": 22,99   "row": 17766100  },101  {102   "path": "EXTRACT/main_functions/debug_utils/get_pixel.m",103   "sha256": "d535544cb107b3ef7ef9ab545910c58a502d6d9b102568e7b49f234e6cbab9f8",104   "language": "MATLAB",105   "lines": 7,106   "truncated": false,107   "block": 22,108   "row": 14494109  },110  {111   "path": "EXTRACT/main_functions/debug_utils/get_pre_correlations.m",112   "sha256": "4c9ac174529f440ef596650e993b8112f992ad37c943f5511fc1bb9a4e105075",113   "language": "MATLAB",114   "lines": 86,115   "truncated": false,116   "block": 22,117   "row": 20632118  },119  {120   "path": "EXTRACT/main_functions/debug_utils/load_h5.m",121   "sha256": "65ab003e91823faf2c20c3148e6b1aa1d06af9a67826aa892f0719c614709b19",122   "language": "MATLAB",123   "lines": 8,124   "truncated": false,125   "block": 22,126   "row": 14569127  },128  {129   "path": "EXTRACT/main_functions/debug_utils/make_figure.m",130   "sha256": "a85feb02d960d909be5f8f35acd5ac14065de8fdfd2798a205a2044a57603878",131   "language": "MATLAB",132   "lines": 2,133   "truncated": false,134   "block": 22,135   "row": 14341136  },137  {138   "path": "EXTRACT/main_functions/debug_utils/plot_bad_cells.m",139   "sha256": "18d4dff658c3fe72c9725dd17ba96b0bfa8a04098a4f3535ddf4476f3d1e1386",140   "language": "MATLAB",141   "lines": 36,142   "truncated": false,143   "block": 22,144   "row": 18730145  },146  {147   "path": "EXTRACT/main_functions/debug_utils/plot_components.m",148   "sha256": "39fdc52856e3c04ba442b1c254e6d0ec92f899bda018b55518887cea0b4f4500",149   "language": "MATLAB",150   "lines": 20,151   "truncated": false,152   "block": 22,153   "row": 15396154  },155  {156   "path": "EXTRACT/main_functions/debug_utils/simulate_data_old.m",157   "sha256": "19023222f934c87c81ecdc9319d85e8a3d232b890794b07eeb10bf621037f9fa",158   "language": "MATLAB",159   "lines": 143,160   "truncated": false,161   "block": 22,162   "row": 21835163  },164  {165   "path": "EXTRACT/main_functions/debug_utils/test_extract.m",166   "sha256": "5a343bc0f4a1bc0af2c9368efa687fac499321d990331a0480e45a0300bb8a4a",167   "language": "MATLAB",168   "lines": 70,169   "truncated": false,170   "block": 22,171   "row": 18731172  },173  {174   "path": "EXTRACT/main_functions/debug_utils/verify_initialization.m",175   "sha256": "3360f801a445f366de764b3141aeb3e7f67598bc968727ee9aefa3320db40214",176   "language": "MATLAB",177   "lines": 53,178   "truncated": false,179   "block": 22,180   "row": 17821181  },182  {183   "path": "EXTRACT/main_functions/debug_utils/visualize_F_goodness.m",184   "sha256": "7acb535dc60769edb2c30fdb9f99645cf916e55e97c3a2330b57cc4c1e533a17",185   "language": "MATLAB",186   "lines": 31,187   "truncated": false,188   "block": 22,189   "row": 16442190  },191  {192   "path": "EXTRACT/main_functions/helper_functions/EXTRACT_output_to_nwb.m",193   "sha256": "2ef69da51c06027c06226583fe3396d8e069734f6c55d4906cf00c66ca2f4a42",194   "language": "MATLAB",195   "lines": 349,196   "truncated": false,197   "block": 22,198   "row": 24339199  },200  {201   "path": "EXTRACT/main_functions/helper_functions/ask_for_label.m",202   "sha256": "2b098a41bcc99ca22a0f786b2a776ad3fb8e723355b331e9216d06173f4dfbb3",203   "language": "MATLAB",204   "lines": 106,205   "truncated": false,206   "block": 22,207   "row": 21197208  },209  {210   "path": "EXTRACT/main_functions/helper_functions/combine_metrics.m",211   "sha256": "0cf96dd0145d16935ad1d7cd3f3e4df28664c8dad450319dcc62b0f8b93b0763",212   "language": "MATLAB",213   "lines": 22,214   "truncated": false,215   "block": 22,216   "row": 16386217  },218  {219   "path": "EXTRACT/main_functions/helper_functions/compute_df.m",220   "sha256": "b6292fd0deec369e0e4b4fd376ed747508db03c2d5ad1767150276c7455a35d1",221   "language": "MATLAB",222   "lines": 37,223   "truncated": false,224   "block": 22,225   "row": 16733226  },227  {228   "path": "EXTRACT/main_functions/helper_functions/compute_lin_part_size.m",229   "sha256": "f2a0b2e0d59ec92ff50c09151512f31a5aed0a598505876f07df1e475ff2464b",230   "language": "MATLAB",231   "lines": 10,232   "truncated": false,233   "block": 22,234   "row": 14838235  },236  {237   "path": "EXTRACT/main_functions/helper_functions/correct_baseline.m",238   "sha256": "ad455af6ec1c2155f321d751ffecbe545670e7e2109dec155fbdef033515f420",239   "language": "MATLAB",240   "lines": 135,241   "truncated": false,242   "block": 22,243   "row": 22025244  },245  {246   "path": "EXTRACT/main_functions/helper_functions/dispfun.m",247   "sha256": "2207c8c65fb8d928ea268aac7e0357702b361c2bd40b8bc668c71312809e2c37",248   "language": "MATLAB",249   "lines": 5,250   "truncated": false,251   "block": 22,252   "row": 14281253  },254  {255   "path": "EXTRACT/main_functions/helper_functions/div_norm_filter.m",256   "sha256": "2ceee8f8aad61edacc78ba445d99e04b8f85349b62cbb2b3e267a9e6e29e1747",257   "language": "MATLAB",258   "lines": 15,259   "truncated": false,260   "block": 22,261   "row": 15800262  },263  {264   "path": "EXTRACT/main_functions/helper_functions/divisive_normalization.m",265   "sha256": "5e0ba1de5ed74f83eb31867f9a9dac30655e70ac3886b955d459774f9cfaf81c",266   "language": "MATLAB",267   "lines": 49,268   "truncated": false,269   "block": 22,270   "row": 17838271  },272  {273   "path": "EXTRACT/main_functions/helper_functions/downsample_space.m",274   "sha256": "9b551d47543253e06662643cfafa029fb881a1e35ba70c68bcf6025297701906",275   "language": "MATLAB",276   "lines": 15,277   "truncated": false,278   "block": 22,279   "row": 15277280  },281  {282   "path": "EXTRACT/main_functions/helper_functions/downsample_time.m",283   "sha256": "600789d666307fc8812b26769a0e0081ceb556afde2749244f6bc306e5e4c73e",284   "language": "MATLAB",285   "lines": 27,286   "truncated": false,287   "block": 22,288   "row": 15845289  },290  {291   "path": "EXTRACT/main_functions/helper_functions/eps_func.m",292   "sha256": "1d5d431637edd56a13da16238ce46a1b645cfb04619a28c3761ce4544ecccc3a",293   "language": "MATLAB",294   "lines": 47,295   "truncated": false,296   "block": 22,297   "row": 17739298  },299  {300   "path": "EXTRACT/main_functions/helper_functions/estimate_avg_radius.m",301   "sha256": "f1e797ad969228bdcac256c9c39b5cca4808680862fd2f4753cd263266f648ad",302   "language": "MATLAB",303   "lines": 17,304   "truncated": false,305   "block": 22,306   "row": 15888307  },308  {309   "path": "EXTRACT/main_functions/helper_functions/estimate_noise_std.m",310   "sha256": "3e420c4613d6a9d97acda03146ed9af7f6a12a12989d1f683c66a18de70eeb34",311   "language": "MATLAB",312   "lines": 90,313   "truncated": false,314   "block": 22,315   "row": 19586316  },317  {318   "path": "EXTRACT/main_functions/helper_functions/estimate_tau.m",319   "sha256": "b2a27fe2b8a06bad8fdb5f72c3ba131b305025b01e1d2108d8b94d022867eee0",320   "language": "MATLAB",321   "lines": 42,322   "truncated": false,323   "block": 22,324   "row": 17251325  },326  {327   "path": "EXTRACT/main_functions/helper_functions/filter_images.m",328   "sha256": "396682977cfd58c611750d4cab4424694426ce08cee6efa7369510a0c64f2a24",329   "language": "MATLAB",330   "lines": 23,331   "truncated": false,332   "block": 22,333   "row": 16348334  },335  {336   "path": "EXTRACT/main_functions/helper_functions/find_conncomp.m",337   "sha256": "a44d01ab5492f0f894c6fd04fd20e0707b7d480e167c1247d77b1aa9cbea7dbd",338   "language": "MATLAB",339   "lines": 33,340   "truncated": false,341   "block": 22,342   "row": 17025343  },344  {345   "path": "EXTRACT/main_functions/helper_functions/find_duplicate_cells.m",346   "sha256": "c96b6f4fd404f19b24ce5e84c312f8ca995c3f608ef567a62e04b411043a217a",347   "language": "MATLAB",348   "lines": 73,349   "truncated": false,350   "block": 22,351   "row": 20339352  },353  {354   "path": "EXTRACT/main_functions/helper_functions/find_spurious_cells.m",355   "sha256": "0394060122bb88e3ac528313d3aa38978295463ea789c6989cb6c6d9d7921bf2",356   "language": "MATLAB",357   "lines": 155,358   "truncated": false,359   "block": 22,360   "row": 22718361  },362  {363   "path": "EXTRACT/main_functions/helper_functions/find_spurious_cells_old.m",364   "sha256": "68ab82d495d40a0289c25aff538e373ee6a7a51c987d09e1111e34581afe1a4f",365   "language": "MATLAB",366   "lines": 60,367   "truncated": false,368   "block": 22,369   "row": 19250370  },371  {372   "path": "EXTRACT/main_functions/helper_functions/fix_zero_spatial_strips.m",373   "sha256": "407282ca4db00c597f41045cdcec2640cdd30de52b8b97c23144fb4fe2c474fa",374   "language": "MATLAB",375   "lines": 65,376   "truncated": false,377   "block": 22,378   "row": 19991379  },380  {381   "path": "EXTRACT/main_functions/helper_functions/generate_images_from_centroids.m",382   "sha256": "f9dc19ccf3a7c98f58f732f8a73682d1802f7313cfaabece5791dd512b4b5ea9",383   "language": "MATLAB",384   "lines": 17,385   "truncated": false,386   "block": 22,387   "row": 15829388  },389  {390   "path": "EXTRACT/main_functions/helper_functions/generate_init_image.m",391   "sha256": "046a1d89998df1dfe78ab508ea1f2c9401a10d47fa5acd96962f7e2a7124bed5",392   "language": "MATLAB",393   "lines": 87,394   "truncated": false,395   "block": 22,396   "row": 20696397  },398  {399   "path": "EXTRACT/main_functions/helper_functions/getEXTRACTsampleData.m",400   "sha256": "eda1be4dbd44f9491ba55f1c68f3bb80c79aa2b040dbe83be3c81524c5254780",401   "language": "MATLAB",402   "lines": 33,403   "truncated": false,404   "block": 22,405   "row": 17727406  },407  {408   "path": "EXTRACT/main_functions/helper_functions/get_active_frames.m",409   "sha256": "e98e98ed17ab29ed9e63b217bfa6fddc2f353a8de1729098ce01f4b08031ed17",410   "language": "MATLAB",411   "lines": 40,412   "truncated": false,413   "block": 22,414   "row": 17607415  },416  {417   "path": "EXTRACT/main_functions/helper_functions/get_arbitrary_mask.m",418   "sha256": "900fcf3166d329f497df9c901db63c8e243a970e2b2e7ad10a0c616ac1cd08b5",419   "language": "MATLAB",420   "lines": 17,421   "truncated": false,422   "block": 22,423   "row": 15328424  },425  {426   "path": "EXTRACT/main_functions/helper_functions/get_cell_areas.m",427   "sha256": "b4f81e0fa2723c4f5386799226c7a50dc8f7b3233257b14323590ea9819f66ea",428   "language": "MATLAB",429   "lines": 9,430   "truncated": false,431   "block": 22,432   "row": 14406433  },434  {435   "path": "EXTRACT/main_functions/helper_functions/get_cellcheck_features.m",436   "sha256": "96e5401d2c1a8ee0842bb16bc7d978824ae5d5954850b83dbc1ca3a89647b6fd",437   "language": "MATLAB",438   "lines": 7,439   "truncated": false,440   "block": 22,441   "row": 14576442  },443  {444   "path": "EXTRACT/main_functions/helper_functions/get_circular_mask.m",445   "sha256": "98cc1941b8a3040b1287201881c4155dd6a2151b90cca4c04a7fa9c0e8697d95",446   "language": "MATLAB",447   "lines": 60,448   "truncated": false,449   "block": 20,450   "row": 9882451  },452  {453   "path": "EXTRACT/main_functions/helper_functions/get_circular_mask_old.m",454   "sha256": "29dba59d76b932052c59fadecbe952de1fc7d85416547036db66ca95f4fec68a",455   "language": "MATLAB",456   "lines": 25,457   "truncated": false,458   "block": 22,459   "row": 16782460  },461  {462   "path": "EXTRACT/main_functions/helper_functions/get_circularity_metrics.m",463   "sha256": "403c032ed4b8989130f72a7786ecbeb8a95c2f60286fd8c3ae6d82e527730a0a",464   "language": "MATLAB",465   "lines": 26,466   "truncated": false,467   "block": 22,468   "row": 17102469  },470  {471   "path": "EXTRACT/main_functions/helper_functions/get_current_partition.m",472   "sha256": "1cfdc2d37ff8b87b084e8357a1ba8e3c9c9eede95c9923b5f3fc98c3ed6e1aa3",473   "language": "MATLAB",474   "lines": 59,475   "truncated": false,476   "block": 22,477   "row": 19641478  },479  {480   "path": "EXTRACT/main_functions/helper_functions/get_eccentricity_metric.m",481   "sha256": "9b0aa70b987dbf14c5eb42666847b2c583ca5f9416badf07c0c685382eb8f700",482   "language": "MATLAB",483   "lines": 5,484   "truncated": false,485   "block": 22,486   "row": 14507487  },488  {489   "path": "EXTRACT/main_functions/helper_functions/get_free_mem.m",490   "sha256": "2c874c0eba80ba80e39804632c128cde7143f6ee8c5c4ec2a8e8a57fdee07d83",491   "language": "MATLAB",492   "lines": 14,493   "truncated": false,494   "block": 22,495   "row": 15283496  },497  {498   "path": "EXTRACT/main_functions/helper_functions/get_im_boundary.m",499   "sha256": "b251418abab4abea7df5909f39ed9e72c0b12ebfff442ad8c83a736634402bec",500   "language": "MATLAB",501   "lines": 12,502   "truncated": false,503   "block": 22,504   "row": 15013505  },506  {507   "path": "EXTRACT/main_functions/helper_functions/get_image_axis_lengths.m",508   "sha256": "d58da33ff92b7a26e01d0a4f2ba877cbbf37c18dc3ce36a912c4bf6213131bfb",509   "language": "MATLAB",510   "lines": 20,511   "truncated": false,512   "block": 22,513   "row": 16179514  },515  {516   "path": "EXTRACT/main_functions/helper_functions/get_image_xy_ranges.m",517   "sha256": "f652aaa506b16f67fdf6bc8dfd86b02e590ce67b68f56452b5d969a6124e79bf",518   "language": "MATLAB",519   "lines": 11,520   "truncated": false,521   "block": 22,522   "row": 15156523  },524  {525   "path": "EXTRACT/main_functions/helper_functions/get_movie_size.m",526   "sha256": "558a55ffc31690dcea78995e317eda606af4992eb490f72158fc8600d549ee76",527   "language": "MATLAB",528   "lines": 10,529   "truncated": false,530   "block": 22,531   "row": 14905532  },533  {534   "path": "EXTRACT/main_functions/helper_functions/get_quality_metric_map.m",535   "sha256": "49096dd70905fb20c063545c886cc203ef7e6f6b8a76538ee934d774bb0546e9",536   "language": "MATLAB",537   "lines": 13,538   "truncated": false,539   "block": 22,540   "row": 16403541  },542  {543   "path": "EXTRACT/main_functions/helper_functions/get_st_corr.m",544   "sha256": "d3fb4e142f44ad972d242f30d4dc2a3c62ce18d80bbe9750a6d0d36e61604e80",545   "language": "MATLAB",546   "lines": 79,547   "truncated": false,548   "block": 22,549   "row": 20052550  },551  {552   "path": "EXTRACT/main_functions/helper_functions/get_st_corr_metrics.m",553   "sha256": "3768def02eea2492f6a0adad620ae5df6ba9cf2434d3259a0da5b28561f00b94",554   "language": "MATLAB",555   "lines": 19,556   "truncated": false,557   "block": 22,558   "row": 15459559  },560  {561   "path": "EXTRACT/main_functions/helper_functions/get_summary_stack.m",562   "sha256": "ff76ed32b849f2db968b10ac14737a96a3e7460ffb2031f4828f02669f877376",563   "language": "MATLAB",564   "lines": 38,565   "truncated": false,566   "block": 22,567   "row": 18342568  },569  {570   "path": "EXTRACT/main_functions/helper_functions/get_trace_noise.m",571   "sha256": "e8d29ff58c5bc5730fe5f97eac50449ed359e86f92ff2736bfa59d30cfa64c37",572   "language": "MATLAB",573   "lines": 50,574   "truncated": false,575   "block": 22,576   "row": 17863577  },578  {579   "path": "EXTRACT/main_functions/helper_functions/get_trace_snr.m",580   "sha256": "38ce1a0c250e697284a5fcdeba1340484ba28ce2d71eacec7df663a73089cd7e",581   "language": "MATLAB",582   "lines": 14,583   "truncated": false,584   "block": 22,585   "row": 14696586  },587  {588   "path": "EXTRACT/main_functions/helper_functions/guess_labels_from_metrics.m",589   "sha256": "98b013291a87d1bf09799ca3a988c9092a614710f4a929d1aa5b291c70d5413c",590   "language": "MATLAB",591   "lines": 35,592   "truncated": false,593   "block": 22,594   "row": 17713595  },596  {597   "path": "EXTRACT/main_functions/helper_functions/ica_finetune.m",598   "sha256": "3da7b64e9861889479fbfeaa1cfe2c9627a58070cf4ee44188794cf3300ae5a9",599   "language": "MATLAB",600   "lines": 34,601   "truncated": false,602   "block": 22,603   "row": 17217604  },605  {606   "path": "EXTRACT/main_functions/helper_functions/imwiener.m",607   "sha256": "a7f8baa8c4616fea3c11df2d856b2b7820a7a488ed1a62f1e174813832218e4d",608   "language": "MATLAB",609   "lines": 70,610   "truncated": false,611   "block": 22,612   "row": 19084613  },614  {615   "path": "EXTRACT/main_functions/helper_functions/ismatlabonline.m",616   "sha256": "191859a7db3dba8f8e82152af392fa078be846410f66d569512bf3821fd00c1c",617   "language": "MATLAB",618   "lines": 14,619   "truncated": false,620   "block": 22,621   "row": 15105622  },623  {624   "path": "EXTRACT/main_functions/helper_functions/kappa_of_epsilon.m",625   "sha256": "fe3b4be5970a5bd9ff09fa1e059607649e514a275674ef6b429cc7934033c49f",626   "language": "MATLAB",627   "lines": 22,628   "truncated": false,629   "block": 22,630   "row": 16367631  },632  {633   "path": "EXTRACT/main_functions/helper_functions/label_components.m",634   "sha256": "8baf4a287a4d38a1b7232f409fa31750613a887cf2fd81e311f4759e1073f9da",635   "language": "MATLAB",636   "lines": 47,637   "truncated": false,638   "block": 22,639   "row": 19291640  },641  {642   "path": "EXTRACT/main_functions/helper_functions/make_mask.m",643   "sha256": "92f6c440bd7c9ca00f5b5740807349fc2f77221c000e03a87e76acbda4460880",644   "language": "MATLAB",645   "lines": 9,646   "truncated": false,647   "block": 22,648   "row": 15024649  },650  {651   "path": "EXTRACT/main_functions/helper_functions/match_sets.m",652   "sha256": "2bb5b4e2cb3ea7d2aaac03a6655f8b1d322f79e1a8a23f0a8894382a5ac8667b",653   "language": "MATLAB",654   "lines": 70,655   "truncated": false,656   "block": 22,657   "row": 18232658  },659  {660   "path": "EXTRACT/main_functions/helper_functions/maybe_gpu.m",661   "sha256": "1016e3a3a2f63cae752793dd5ffa242c0e00f9295a0cd969264a8979c721f738",662   "language": "MATLAB",663   "lines": 9,664   "truncated": false,665   "block": 22,666   "row": 14666667  },668  {669   "path": "EXTRACT/main_functions/helper_functions/medfilt_outliers.m",670   "sha256": "84cfba423e0c2b444a24c2d52733dcc1985aa5f29d998d1886f09d5c3ea22a6c",671   "language": "MATLAB",672   "lines": 26,673   "truncated": false,674   "block": 22,675   "row": 17194676  },677  {678   "path": "EXTRACT/main_functions/helper_functions/ml_predict_labels.m",679   "sha256": "972804fda8fec40dd7d817769122e8112b17884515f3ea5ee9f7e792c11087ea",680   "language": "MATLAB",681   "lines": 28,682   "truncated": false,683   "block": 22,684   "row": 16963685  },686  {687   "path": "EXTRACT/main_functions/helper_functions/ndSparse.m",688   "sha256": "bd0cf589d9958487680900e5353fbdfbe892b1da90dc741f483f01324920dd03",689   "language": "MATLAB",690   "lines": 2951,691   "truncated": false,692   "block": 22,693   "row": 25079694  },695  {696   "path": "EXTRACT/main_functions/helper_functions/normalize_to_one.m",697   "sha256": "031ca553de8175b34d0b77fca6427a85bc0d83cf8470e28abbb2abdc33558c56",698   "language": "MATLAB",699   "lines": 5,700   "truncated": false,701   "block": 22,702   "row": 14472703  },704  {705   "path": "EXTRACT/main_functions/helper_functions/parse_movie_name.m",706   "sha256": "9a1a7ecee41ddcafb715bbd4e22f246990408f1c9641c1d986824edc72aa008a",707   "language": "MATLAB",708   "lines": 23,709   "truncated": false,710   "block": 22,711   "row": 15858712  },713  {714   "path": "EXTRACT/main_functions/helper_functions/peakseek.m",715   "sha256": "c03d7caa7239323b8fa0b3f56eb0b0315804189216fa46294f8ee2c854209970",716   "language": "MATLAB",717   "lines": 50,718   "truncated": false,719   "block": 22,720   "row": 17530721  },722  {723   "path": "EXTRACT/main_functions/helper_functions/plot_cell_images.m",724   "sha256": "c593ebba5e85cf3269a857671ecb5115417c94ee96db48e7bb90012a59ed5307",725   "language": "MATLAB",726   "lines": 68,727   "truncated": false,728   "block": 22,729   "row": 19414730  },731  {732   "path": "EXTRACT/main_functions/helper_functions/preprocess_movie.m",733   "sha256": "58196553b65d27b0d940a302c75791033dc870edcbbd9d2624d1fcabb35a2315",734   "language": "MATLAB",735   "lines": 72,736   "truncated": false,737   "block": 22,738   "row": 19503739  },740  {741   "path": "EXTRACT/main_functions/helper_functions/remove_redundant.m",742   "sha256": "18347e065e6a7df2fa82d3520ea973024b36e499ba9b7dbf6034b98c2c898814",743   "language": "MATLAB",744   "lines": 204,745   "truncated": false,746   "block": 22,747   "row": 23531748  },749  {750   "path": "EXTRACT/main_functions/helper_functions/remove_zero_edge_pixels.m",751   "sha256": "f75e0e9f04553c2846ed89f56e1f741063fe7094277ba37481558c4329d3f516",752   "language": "MATLAB",753   "lines": 48,754   "truncated": false,755   "block": 22,756   "row": 18855757  },758  {759   "path": "EXTRACT/main_functions/helper_functions/replace_nans_with_zeros.m",760   "sha256": "3c10ca209dd197615ba540c1554ba501ed398e8c42de414b1b35fb9ef8a4d647",761   "language": "MATLAB",762   "lines": 13,763   "truncated": false,764   "block": 22,765   "row": 14770766  },767  {768   "path": "EXTRACT/main_functions/helper_functions/select_indices.m",769   "sha256": "1a9d8fe732c3eea0ae6a864dd8979b936db2409457f595e97f18e96b6324f186",770   "language": "MATLAB",771   "lines": 5,772   "truncated": false,773   "block": 22,774   "row": 14622775  },776  {777   "path": "EXTRACT/main_functions/helper_functions/smooth_images.m",778   "sha256": "a6acbe76e024736a45741eb9a57e8f210ddc48aba5f0d58e4e129f15c2eac9b8",779   "language": "MATLAB",780   "lines": 32,781   "truncated": false,782   "block": 22,783   "row": 17451784  },785  {786   "path": "EXTRACT/main_functions/helper_functions/smooth_traces.m",787   "sha256": "73c9f56e4e053ccf1ce64da22da0dcdfef20a05a67d20f1ac1a68602fab78a23",788   "language": "MATLAB",789   "lines": 10,790   "truncated": false,791   "block": 22,792   "row": 14867793  },794  {795   "path": "EXTRACT/main_functions/helper_functions/spat_corruption.m",796   "sha256": "1488c3819e8dd70ca3000848f384fed598b50a644e2c4e4c17c5b0c0264552f1",797   "language": "MATLAB",798   "lines": 122,799   "truncated": false,800   "block": 22,801   "row": 21537802  },803  {804   "path": "EXTRACT/main_functions/helper_functions/spatial_bandpass.m",805   "sha256": "7e622c3aa361f1cf8f59fbfbd109a7e5ac6076825752cccd902897f5cf37148a",806   "language": "MATLAB",807   "lines": 116,808   "truncated": false,809   "block": 22,810   "row": 20855811  },812  {813   "path": "EXTRACT/main_functions/helper_functions/spatial_gauss_lowpass.m",814   "sha256": "2de93bb36d54c55118c3bf6e82ff361fc63a5879ce41e29c450bcf4b65f4ccb6",815   "language": "MATLAB",816   "lines": 90,817   "truncated": false,818   "block": 22,819   "row": 19856820  },821  {822   "path": "EXTRACT/main_functions/helper_functions/swt_denoise.m",823   "sha256": "a85f9f19ca48900beec89c7925f0ab4ed3103a5e6e28549c73b87c5779898125",824   "language": "MATLAB",825   "lines": 30,826   "truncated": false,827   "block": 22,828   "row": 16390829  },830  {831   "path": "EXTRACT/main_functions/helper_functions/temporal_corruption.m",832   "sha256": "100cf7f4080f549a2ae613291471c061dede66eaf036fd9680309b01a14e66c0",833   "language": "MATLAB",834   "lines": 14,835   "truncated": false,836   "block": 22,837   "row": 15309838  },839  {840   "path": "EXTRACT/main_functions/helper_functions/temporal_denoising.m",841   "sha256": "70f4e6aef046c2e51706a9bcdc993aa7200308b3b3e8a9f5f00821a50c8d91d1",842   "language": "MATLAB",843   "lines": 64,844   "truncated": false,845   "block": 22,846   "row": 18901847  },848  {849   "path": "EXTRACT/main_functions/helper_functions/temporal_matched_filter.m",850   "sha256": "1fffb172df93cf22d5459037bca5c3f3c699aaf0311594acc2e371d33d8950dd",851   "language": "MATLAB",852   "lines": 11,853   "truncated": false,854   "block": 22,855   "row": 14796856  },857  {858   "path": "EXTRACT/main_functions/helper_functions/update_merged_images.m",859   "sha256": "62ee57a63d4af0cfa58f68aa86c9162bdd5a0a2a8c0de35d77297cea7e28923b",860   "language": "MATLAB",861   "lines": 9,862   "truncated": false,863   "block": 22,864   "row": 15023865  },866  {867   "path": "EXTRACT/main_functions/helper_functions/upsample_traces.m",868   "sha256": "e4ad1b6d5fe6e288a245e016009a211cb576ba9d3f9a93f7b4c160b31c723a21",869   "language": "MATLAB",870   "lines": 9,871   "truncated": false,872   "block": 22,873   "row": 14889874  },875  {876   "path": "EXTRACT/main_functions/solvers/base solvers for multiple cells/fp_solve.m",877   "sha256": "0a3d14c38a82c8ecbca9ec557137f569879b2d45fad96d9e3e4eb0b8cb2fa900",878   "language": "MATLAB",879   "lines": 48,880   "truncated": false,881   "block": 22,882   "row": 16590883  },884  {885   "path": "EXTRACT/main_functions/solvers/base solvers for multiple cells/fp_solve_adaptive.m",886   "sha256": "1e3b5a79275d4eb164afece5bd0e00114209ad01145c7c0c3ed85aa13d94cf29",887   "language": "MATLAB",888   "lines": 186,889   "truncated": false,890   "block": 22,891   "row": 22126892  },893  {894   "path": "EXTRACT/main_functions/solvers/base solvers for multiple cells/fp_solve_adaptive_baseline.m",895   "sha256": "99865ca6b60e567cb8a1bc1ef6a029af7e26ed9be4783b6b8558239d6619ca16",896   "language": "MATLAB",897   "lines": 198,898   "truncated": false,899   "block": 22,900   "row": 22302901  },902  {903   "path": "EXTRACT/main_functions/solvers/base solvers for multiple cells/fp_solve_adaptive_filter.m",904   "sha256": "40d066137224f43b9c7862f4ab3718689f78b2ee756ace986fe2b9b5e47b78bb",905   "language": "MATLAB",906   "lines": 189,907   "truncated": false,908   "block": 22,909   "row": 22176910  },911  {912   "path": "EXTRACT/main_functions/solvers/base solvers for multiple cells/fp_solve_adaptive_raw.m",913   "sha256": "1559b1722d28c99594fa135e4f7a6686bbb68998c12c4b15ddd31ab2bcdb4957",914   "language": "MATLAB",915   "lines": 186,916   "truncated": false,917   "block": 22,918   "row": 22125919  },920  {921   "path": "EXTRACT/main_functions/solvers/base solvers for multiple cells/fp_solve_admm.m",922   "sha256": "63ae2882977e02ad9f04823e627f818a8a81d9ae9e37fbdb543ad3a4a9e8ee77",923   "language": "MATLAB",924   "lines": 157,925   "truncated": false,926   "block": 22,927   "row": 21209928  },929  {930   "path": "EXTRACT/main_functions/solvers/base solvers for multiple cells/fp_solve_admm_baseline.m",931   "sha256": "b2b07a7b898a436844b0afadee3dcb744d382b251b88f1d20fde25cfa2980b73",932   "language": "MATLAB",933   "lines": 168,934   "truncated": false,935   "block": 22,936   "row": 21366937  },938  {939   "path": "EXTRACT/main_functions/solvers/base solvers for multiple cells/fp_solve_nonneg.m",940   "sha256": "6e81147c0e48ae141af76889ca4d696f844eba9be577d1224d7e8d8804e851f4",941   "language": "MATLAB",942   "lines": 126,943   "truncated": false,944   "block": 22,945   "row": 20159946  },947  {948   "path": "EXTRACT/main_functions/solvers/cell finding solvers/alt_opt_single.m",949   "sha256": "e14eb6901f6886bf303d25d899083ba367d8e8c9305c8a52afaa3a0c1f2bf509",950   "language": "MATLAB",951   "lines": 124,952   "truncated": false,953   "block": 22,954   "row": 21292955  },956  {957   "path": "EXTRACT/main_functions/solvers/cell finding solvers/solve_single_source.m",958   "sha256": "581abb2b68543c3676937bc681bfdc857724fdd3f0e5b889bac98016b3319ebc",959   "language": "MATLAB",960   "lines": 28,961   "truncated": false,962   "block": 22,963   "row": 16328964  },965  {966   "path": "EXTRACT/main_functions/solvers/cell finding solvers/solve_single_source_adaptive.m",967   "sha256": "872fcf358a03f9df1f05a12c1d989674d916253a664c7f5e1c61031b7dbd0306",968   "language": "MATLAB",969   "lines": 77,970   "truncated": false,971   "block": 22,972   "row": 19402973  },974  {975   "path": "EXTRACT/main_functions/solvers/cell refinement + frr solvers/solve_S.m",976   "sha256": "fb4352fdf06c49439ec45d9f7359eecce152c233993dfacf91e6fcb2aab26fdd",977   "language": "MATLAB",978   "lines": 94,979   "truncated": false,980   "block": 22,981   "row": 21405982  },983  {984   "path": "EXTRACT/main_functions/solvers/cell refinement + frr solvers/solve_T.m",985   "sha256": "6337cf5fcbbfcb8bc1c85c8d7dec7a98f00e348decbdb2736a77923a5979f78a",986   "language": "MATLAB",987   "lines": 85,988   "truncated": false,989   "block": 22,990   "row": 20753991  },992  {993   "path": "EXTRACT/main_functions/solvers/cell refinement + frr solvers/solve_T_robust.m",994   "sha256": "f4e32d35a22d7423d4b544f004d78b20c45d7e964adb6dac8757509a3a87560a",995   "language": "MATLAB",996   "lines": 116,997   "truncated": false,998   "block": 22,999   "row": 215631000  },1001  {1002   "path": "EXTRACT/modules/cell_check.m",1003   "sha256": "e7faa1e1a8b6621ff0c9205462f966e8c350e7322b35a6f6319907828c4a209d",1004   "language": "MATLAB",1005   "lines": 1054,1006   "truncated": false,1007   "block": 22,1008   "row": 249391009  },1010  {1011   "path": "EXTRACT/modules/cw_extract.m",1012   "sha256": "a0a3e677c04201866461aeffd949e0bfbbe8e88cc899f0414b140fc792d28eff",1013   "language": "MATLAB",1014   "lines": 432,1015   "truncated": false,1016   "block": 22,1017   "row": 242691018  },1019  {1020   "path": "EXTRACT/modules/extractor.m",1021   "sha256": "4ff8b30f7276708454adeecf547d4a28290f5d1becb1bd8dd4934c4acb50bd4b",1022   "language": "MATLAB",1023   "lines": 566,1024   "truncated": false,1025   "block": 22,1026   "row": 246341027  },1028  {1029   "path": "EXTRACT/modules/final_robust_run.m",1030   "sha256": "7e6ef8fc4a059ee3780e84904aa68c77d1a7002a0000a28b7e24c25f46a2dba1",1031   "language": "MATLAB",1032   "lines": 32,1033   "truncated": false,1034   "block": 22,1035   "row": 177591036  },1037  {1038   "path": "EXTRACT/modules/plot_hyperparameter_curves.m",1039   "sha256": "0851d51e0b341b9b949b9c3951db4448eeb845784feb238968576d40bb07680a",1040   "language": "MATLAB",1041   "lines": 91,1042   "truncated": false,1043   "block": 22,1044   "row": 199121045  },1046  {1047   "path": "EXTRACT/modules/preprocess_save.m",1048   "sha256": "60c745e049653615892c5450ea4fe54af086b66213d205967ca1c72f8617c58b",1049   "language": "MATLAB",1050   "lines": 138,1051   "truncated": false,1052   "block": 22,1053   "row": 214061054  },1055  {1056   "path": "EXTRACT/modules/run_extract.m",1057   "sha256": "8949c2d920577953dc9b3245263adf9ed0f43b0daed7a6f29b83b05df0a11aa6",1058   "language": "MATLAB",1059   "lines": 1113,1060   "truncated": false,1061   "block": 22,1062   "row": 249551063  },1064  {1065   "path": "EXTRACT/summary functions/plot_cells_overlay.m",1066   "sha256": "22bc36c6db8d1a3036349832b28b2305201744822824116f9b1e2ed3043b0444",1067   "language": "MATLAB",1068   "lines": 49,1069   "truncated": false,1070   "block": 22,1071   "row": 174221072  },1073  {1074   "path": "EXTRACT/summary functions/plot_output_cellmap.m",1075   "sha256": "cf14af528dd2ed5a35e15e2361c4c6bbf5d206e91f8b04fdf427974d6130babb",1076   "language": "MATLAB",1077   "lines": 90,1078   "truncated": false,1079   "block": 22,1080   "row": 208201081  },1082  {1083   "path": "EXTRACT/summary functions/view_movie.m",1084   "sha256": "9d6b2542c8472db014ab69c2d286ddc61a1df55c835e98a7608ddce9271d2c93",1085   "language": "MATLAB",1086   "lines": 124,1087   "truncated": false,1088   "block": 22,1089   "row": 211511090  },1091  {1092   "path": "External algorithms/Template scripts/downsample_and_run_extract.m",1093   "sha256": "7cd65505ac7050dd60105462adab1e3dfa994649398cc4192d47e74dd3e3d4c0",1094   "language": "MATLAB",1095   "lines": 56,1096   "truncated": false,1097   "block": 22,1098   "row": 183861099  },1100  {1101   "path": "External algorithms/Template scripts/motion_correction_script.m",1102   "sha256": "d44f037790b21e8de58abc0ead82e000c25d23cacc434b6c838812805c141f4a",1103   "language": "MATLAB",1104   "lines": 38,1105   "truncated": false,1106   "block": 22,1107   "row": 176631108  },1109  {1110   "path": "External algorithms/cropmovie_pipeline.m",1111   "sha256": "1437e9b948530a518065a8db05b9a846e3d2a09fb1f505294d73e906c65f68d9",1112   "language": "MATLAB",1113   "lines": 126,1114   "truncated": false,1115   "block": 22,1116   "row": 206591117  },1118  {1119   "path": "External algorithms/downsamplespace_pipeline.m",1120   "sha256": "f5aec0ed1434b4ebde1aea9fc24c3a52aae7ff858b9a49cd58c576f32fd6e642",1121   "language": "MATLAB",1122   "lines": 108,1123   "truncated": false,1124   "block": 22,1125   "row": 201901126  },1127  {1128   "path": "External algorithms/downsampletime_pipeline.m",1129   "sha256": "230961413891ff4dcc6589a869b7340cc84c5e0d7c6b1c1efd1f3c645127518f",1130   "language": "MATLAB",1131   "lines": 67,1132   "truncated": false,1133   "block": 22,1134   "row": 185981135  },1136  {1137   "path": "External algorithms/get_defaults_mc.m",1138   "sha256": "8b892e820d2a03a40621051d106072d8607f92ebffeba79865020505ae35978f",1139   "language": "MATLAB",1140   "lines": 15,1141   "truncated": false,1142   "block": 22,1143   "row": 165701144  },1145  {1146   "path": "External algorithms/get_mask.m",1147   "sha256": "8c3a96d725f5cd55a356f064a297849a5236645ea213e78bb162a29e2930a248",1148   "language": "MATLAB",1149   "lines": 20,1150   "truncated": false,1151   "block": 22,1152   "row": 150041153  },1154  {1155   "path": "External algorithms/parfor_progress/ParforProgressbar.m",1156   "sha256": "1a9284c41bcc35409ca0d8f035a429b0565b078e00f8165d2de5bdb5563dd390",1157   "language": "MATLAB",1158   "lines": 343,1159   "truncated": false,1160   "block": 6,1161   "row": 183981162  },1163  {1164   "path": "External algorithms/parfor_progress/progressbar.m",1165   "sha256": "15a19b8b9b236b5febefca1dbf547afd15d2cbae0bfe6d087398eec99f835f5e",1166   "language": "MATLAB",1167   "lines": 359,1168   "truncated": false,1169   "block": 6,1170   "row": 179181171  },1172  {1173   "path": "External algorithms/parfor_progress/testParforProgressbar.m",1174   "sha256": "ca78646c016de625debcef3fde07ea055da21c872059ec57d35950ecf05e9774",1175   "language": "MATLAB",1176   "lines": 56,1177   "truncated": false,1178   "block": 6,1179   "row": 97021180  },1181  {1182   "path": "External algorithms/progressbar/progressbar.m",1183   "sha256": "15a19b8b9b236b5febefca1dbf547afd15d2cbae0bfe6d087398eec99f835f5e",1184   "language": "MATLAB",1185   "lines": 359,1186   "truncated": false,1187   "block": 6,1188   "row": 179181189  },1190  {1191   "path": "External algorithms/read_from_tif.m",1192   "sha256": "d5190f99dab60ff2e6f7c7356edf5e5f72b444d07fa2ebe9958b087ae7e1e70b",1193   "language": "MATLAB",1194   "lines": 21,1195   "truncated": false,1196   "block": 22,1197   "row": 149271198  },1199  {1200   "path": "External algorithms/run_normcorre_pipeline.m",

Showing the first 1,200 of 1497 lines. Download the file for the rest.