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.
05.6k
1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/cardiovascular-modeling-laboratory/zlinedetection",4 "url": "https://github.com/Cardiovascular-Modeling-Laboratory/zlineDetection",5 "host": "github.com",6 "commit": "682df56d5248f631796234391bc4f985799a8cef",7 "license": "BSD-3-Clause",8 "license_confirmed_by": "license file LICENSE.txt",9 "redistribution": "yes",10 "files": [11 {12 "path": "LICENSE.txt",13 "sha256": "4a16965804e13a5b542efcb5101e82d9b9bee1d1e90004da9ed7f2de98e7474e",14 "language": "License",15 "lines": 69,16 "truncated": false,17 "block": 14,18 "row": 1720319 },20 {21 "path": "MerlinRenameScript.m",22 "sha256": "87ba4095392333a2e3253588b6b511e29bba31936a5719091ae8a56d1dfb011a",23 "language": "MATLAB",24 "lines": 78,25 "truncated": false,26 "block": 14,27 "row": 2470228 },29 {30 "path": "README.md",31 "sha256": "1be78e92f043345c9bb060661c8a468af8b55e5b762eda2547e8ac66d54e7503",32 "language": "Text",33 "lines": 55,34 "truncated": false,35 "block": 16,36 "row": 718837 },38 {39 "path": "functions/CSmanualBackgroundrmv.m",40 "sha256": "a17fd1ff3c4294693884a456008fbf885cb04987e0818a5e78ca65c763ecbd4f",41 "language": "MATLAB",42 "lines": 424,43 "truncated": false,44 "block": 15,45 "row": 392746 },47 {48 "path": "functions/RUNzlineDetection.m",49 "sha256": "1a63250fb03d9ed8a883571fc54b9889c8568ed548d9eebf417784b16bd75ce8",50 "language": "MATLAB",51 "lines": 249,52 "truncated": false,53 "block": 15,54 "row": 308955 },56 {57 "path": "functions/YBiter.m",58 "sha256": "44e5cea463dfaaeae0b51994482321f3b4c7ee3d23ec034d5cb809fd42c5f2da",59 "language": "MATLAB",60 "lines": 69,61 "truncated": false,62 "block": 14,63 "row": 2151064 },65 {66 "path": "functions/actin_filtering/actinDetection.m",67 "sha256": "77dfb95eb7af20110202fcfc11979f974783524a743dfb61c72a079e66079e25",68 "language": "MATLAB",69 "lines": 119,70 "truncated": false,71 "block": 15,72 "row": 50573 },74 {75 "path": "functions/actin_filtering/actinExplorePlots.m",76 "sha256": "4c857e1c5de9467b8fa76a2685bf9d6055ff07e337614525c7014646d1b775d7",77 "language": "MATLAB",78 "lines": 117,79 "truncated": false,80 "block": 15,81 "row": 68982 },83 {84 "path": "functions/actin_filtering/actinOrientationVectors_TEST.m",85 "sha256": "e206b1e5ea5e01a9db008313417449bafddb91c0d2c871454ea0d6264fe3d30b",86 "language": "MATLAB",87 "lines": 39,88 "truncated": false,89 "block": 14,90 "row": 2189091 },92 {93 "path": "functions/actin_filtering/createActinMask.m",94 "sha256": "cd1e3d9ef867b129261aa84490a69f1321d5773fb31c06a366c89827cfb48c6f",95 "language": "MATLAB",96 "lines": 20,97 "truncated": false,98 "block": 14,99 "row": 18527100 },101 {102 "path": "functions/actin_filtering/exploreFilterWithActin.m",103 "sha256": "db7d4e93126efdde6cc21a63578091ce8ad35084c57bd17f5aab8308fd6cbd81",104 "language": "MATLAB",105 "lines": 318,106 "truncated": false,107 "block": 15,108 "row": 3490109 },110 {111 "path": "functions/actin_filtering/filterWithActin.m",112 "sha256": "d9af771326c4996d2d0ff0f5e2da3248c7886c7d6ebce407a32f0f86d440c35b",113 "language": "MATLAB",114 "lines": 121,115 "truncated": false,116 "block": 15,117 "row": 736118 },119 {120 "path": "functions/actin_filtering/gridDirector.m",121 "sha256": "d13d879ec6a09e95dd54ca59429bfd21becc0bb06b722cc8848c120221d8b2a0",122 "language": "MATLAB",123 "lines": 136,124 "truncated": false,125 "block": 15,126 "row": 501127 },128 {129 "path": "functions/actin_filtering/plotOrientationVectors.m",130 "sha256": "65542a53d4f72a085c6258250ab85dabecea46d5b91288e7454107d84e8df4eb",131 "language": "MATLAB",132 "lines": 42,133 "truncated": false,134 "block": 14,135 "row": 20364136 },137 {138 "path": "functions/addDirectory.m",139 "sha256": "d07306811f8658382f9b09a5f3b479c24fb67afe275c28a98ed59f7a4e251fe2",140 "language": "MATLAB",141 "lines": 68,142 "truncated": false,143 "block": 14,144 "row": 22904145 },146 {147 "path": "functions/additionalUserInput.m",148 "sha256": "ef9cc43b18127311b58c767ba049d61209f8ebc7aec9cb11d8ce271dc25decb5",149 "language": "MATLAB",150 "lines": 244,151 "truncated": false,152 "block": 15,153 "row": 2665154 },155 {156 "path": "functions/analyzeImage.m",157 "sha256": "be1bc604f04d11d4427fb67fd067745ff52e478fddf1eda1f292fb163110578e",158 "language": "MATLAB",159 "lines": 282,160 "truncated": false,161 "block": 15,162 "row": 3267163 },164 {165 "path": "functions/appendFilename.m",166 "sha256": "f5b36a7dd41748eb4cb6a9a302b915f7006dacfe615e0c43fea38e6b781187f0",167 "language": "MATLAB",168 "lines": 61,169 "truncated": false,170 "block": 14,171 "row": 21884172 },173 {174 "path": "functions/automateParameterExploration.m",175 "sha256": "79ae1f34d53dd4076a77acad6413560400c004afddcdaa00bcdf6db27910ce5d",176 "language": "MATLAB",177 "lines": 195,178 "truncated": false,179 "block": 15,180 "row": 2104181 },182 {183 "path": "functions/averageImage.m",184 "sha256": "eb4c7e6f2ecee9a6c6c942993f3f928cf08ba8ba148b8d5e3ed1509640a719c2",185 "language": "MATLAB",186 "lines": 77,187 "truncated": false,188 "block": 14,189 "row": 22599190 },191 {192 "path": "functions/calculateSarcLength.m",193 "sha256": "1d2d0409d7daaa78183e8345d3358be7f413d322eb553958fa2c07e928f6dc89",194 "language": "MATLAB",195 "lines": 172,196 "truncated": false,197 "block": 15,198 "row": 2521199 },200 {201 "path": "functions/calculate_OOP.m",202 "sha256": "efcbe5fe9cbc33d7c553a2c0a335b0c4753b0e57fc209b0e087ad76ceca810c8",203 "language": "MATLAB",204 "lines": 106,205 "truncated": false,206 "block": 15,207 "row": 459208 },209 {210 "path": "functions/cleanSkel.m",211 "sha256": "5a86cb8e4f08dc229db3ab19a5b837a161e20fe071a7ebc0d61a49d976f00767",212 "language": "MATLAB",213 "lines": 90,214 "truncated": false,215 "block": 14,216 "row": 23838217 },218 {219 "path": "functions/coherencefilter_version5b/CoherenceFilter.m",220 "sha256": "353b8dbc058c98e01152e20c5ec53928343007e3c305b8d55035f42e030f64bf",221 "language": "MATLAB",222 "lines": 376,223 "truncated": false,224 "block": 15,225 "row": 3881226 },227 {228 "path": "functions/coherencefilter_version5b/TestCoherenceFilter.m",229 "sha256": "1bc9bcbace319aca9ea763addd0530435e76117dd042667569939cd7f3ace9b2",230 "language": "MATLAB",231 "lines": 386,232 "truncated": false,233 "block": 15,234 "row": 3941235 },236 {237 "path": "functions/coherencefilter_version5b/compile_c_files.m",238 "sha256": "b9a1d03f4d246126de1a6e20a8ace0206181a42dd6da67319b8801643fc0556f",239 "language": "MATLAB",240 "lines": 36,241 "truncated": false,242 "block": 14,243 "row": 20388244 },245 {246 "path": "functions/coherencefilter_version5b/functions/clmp.m",247 "sha256": "6862020c216f77e1d85ce822c2f0657f9fbf4131ee2fd9ccf5a31475ff4c998a",248 "language": "MATLAB",249 "lines": 5,250 "truncated": false,251 "block": 14,252 "row": 17386253 },254 {255 "path": "functions/coherencefilter_version5b/functions/derivative7.m",256 "sha256": "d1b5681e565375eadcfceddbb1f0a8a1e9398796f5317619a110ecd7da4bcc73",257 "language": "MATLAB",258 "lines": 88,259 "truncated": false,260 "block": 15,261 "row": 337262 },263 {264 "path": "functions/coherencefilter_version5b/functions/derivatives.c",265 "sha256": "80e867678a5198261d2ef70280e170db12b10ef223398b5f244073fa68f3c92c",266 "language": "C",267 "lines": 692,268 "truncated": false,269 "block": 14,270 "row": 554271 },272 {273 "path": "functions/coherencefilter_version5b/functions/derivatives.m",274 "sha256": "f6cab48a9e92422b6746ae29b720df7aee5857c017006fde44aa48860ffb5458",275 "language": "MATLAB",276 "lines": 95,277 "truncated": false,278 "block": 14,279 "row": 24750280 },281 {282 "path": "functions/coherencefilter_version5b/functions/imgaussian.c",283 "sha256": "f2e3fbab16f024ace989a8472b9f0c73dd351756709208523bea974d0c81afb5",284 "language": "C",285 "lines": 674,286 "truncated": false,287 "block": 14,288 "row": 549289 },290 {291 "path": "functions/coherencefilter_version5b/functions/imgaussian.m",292 "sha256": "eb8a2b820525b69d05e0ce81e6568c38f127600d02c3f431bbd81276ff52540e",293 "language": "MATLAB",294 "lines": 61,295 "truncated": false,296 "block": 14,297 "row": 23007298 },299 {300 "path": "functions/coherencefilter_version5b/functions/showcs3.m",301 "sha256": "263326b05d79a34e4790f563ac8a87dac671a13542ce8e491f2f393bc089efe0",302 "language": "MATLAB",303 "lines": 218,304 "truncated": false,305 "block": 15,306 "row": 2970307 },308 {309 "path": "functions/coherencefilter_version5b/functions2D/CoherenceFilterStep2D.c",310 "sha256": "fb14a15824286c30ace270971620d4b7de9691fec00871d52d1fcd9a3a51c2c5",311 "language": "C",312 "lines": 173,313 "truncated": false,314 "block": 14,315 "row": 265316 },317 {318 "path": "functions/coherencefilter_version5b/functions2D/CoherenceFilterStep2D.m",319 "sha256": "c3cf2d7f232f41f2e46dda7c6450d63e40bc0729876af9d0d625c3da54576cb2",320 "language": "MATLAB",321 "lines": 16,322 "truncated": false,323 "block": 14,324 "row": 18891325 },326 {327 "path": "functions/coherencefilter_version5b/functions2D/CoherenceFilterStep2D_functions.c",328 "sha256": "c638407756790114055526115d847ffbb0ba9b5de73e86551966b48db7952273",329 "language": "C",330 "lines": 474,331 "truncated": false,332 "block": 14,333 "row": 442334 },335 {336 "path": "functions/coherencefilter_version5b/functions2D/ConstructDiffusionTensor2D.m",337 "sha256": "6ccb5b6a7f80f8423069e76f4611331f00d87f7534479d6698cd18630fcff0e2",338 "language": "MATLAB",339 "lines": 55,340 "truncated": false,341 "block": 14,342 "row": 22666343 },344 {345 "path": "functions/coherencefilter_version5b/functions2D/ConstructDiffusionTensor2DLap.m",346 "sha256": "35a772f83ec2997fa9a654c2074680ce0c19206d8a5506f54344ab3a6be2fe88",347 "language": "MATLAB",348 "lines": 60,349 "truncated": false,350 "block": 14,351 "row": 23314352 },353 {354 "path": "functions/coherencefilter_version5b/functions2D/EigenVectors2D.m",355 "sha256": "98ae2c1224e732d1483ebb70448772c3f382a7b633faa0bfbec3f5a7dfdfd53d",356 "language": "MATLAB",357 "lines": 46,358 "truncated": false,359 "block": 14,360 "row": 21112361 },362 {363 "path": "functions/coherencefilter_version5b/functions2D/EigenVectors2DLap.m",364 "sha256": "8c1550cc54667af8d78f094e129c3ec25bdd8bcf9682d7fa8dfd8b94f47fd831",365 "language": "MATLAB",366 "lines": 46,367 "truncated": false,368 "block": 14,369 "row": 21083370 },371 {372 "path": "functions/coherencefilter_version5b/functions2D/StructureTensor2D.m",373 "sha256": "8a06730ad947a9002e376105077c5e53b653acac45a1d8076372a768e6bf42bb",374 "language": "MATLAB",375 "lines": 19,376 "truncated": false,377 "block": 14,378 "row": 19061379 },380 {381 "path": "functions/coherencefilter_version5b/functions2D/diffusion_scheme_2D_implicit.m",382 "sha256": "53ddc0cf451feb796fa9594ca1277970924339c1d20d92b453157a40a2dec638",383 "language": "MATLAB",384 "lines": 58,385 "truncated": false,386 "block": 14,387 "row": 23302388 },389 {390 "path": "functions/coherencefilter_version5b/functions2D/diffusion_scheme_2D_non_negativity.m",391 "sha256": "3b0ca37b3ba3a2d9fd116c3e969e24d5358fd2ba9cba4c39c7423be600e667ba",392 "language": "MATLAB",393 "lines": 41,394 "truncated": false,395 "block": 14,396 "row": 22508397 },398 {399 "path": "functions/coherencefilter_version5b/functions2D/diffusion_scheme_2D_novel.m",400 "sha256": "7f0801ee7002ea44f2c7a8b65631126fb42f15645d454a3f61aca5249467ac26",401 "language": "MATLAB",402 "lines": 57,403 "truncated": false,404 "block": 14,405 "row": 22640406 },407 {408 "path": "functions/coherencefilter_version5b/functions2D/diffusion_scheme_2D_rotation_invariant.m",409 "sha256": "cdf864f8ccd48ba30c816fff554fffad4f32f4f5903bb3bd501ce9c407a55792",410 "language": "MATLAB",411 "lines": 36,412 "truncated": false,413 "block": 14,414 "row": 20587415 },416 {417 "path": "functions/coherencefilter_version5b/functions2D/diffusion_scheme_2D_standard.m",418 "sha256": "2408097c1e8d47bd87a2f066d317bade707e94aba24164797194de03e1e06a8e",419 "language": "MATLAB",420 "lines": 36,421 "truncated": false,422 "block": 14,423 "row": 21423424 },425 {426 "path": "functions/coherencefilter_version5b/functions2D/hessian.m",427 "sha256": "e7fb7969957e6b2bef90ac780a2d697e134d3bec9fdd244f249c83f783c96684",428 "language": "MATLAB",429 "lines": 29,430 "truncated": false,431 "block": 14,432 "row": 19217433 },434 {435 "path": "functions/coherencefilter_version5b/functions2D/ut_gauss.m",436 "sha256": "de3fb2a25563202efb670b135f38929152bcdf3a835d04205ae24494bd23fb54",437 "language": "MATLAB",438 "lines": 191,439 "truncated": false,440 "block": 15,441 "row": 1849442 },443 {444 "path": "functions/coherencefilter_version5b/functions3D/CoherenceFilterStep3D.c",445 "sha256": "e7aef53958701fb255a08bc7b22bd360335bd089445aa22ff363971cd5748556",446 "language": "C",447 "lines": 218,448 "truncated": false,449 "block": 14,450 "row": 328451 },452 {453 "path": "functions/coherencefilter_version5b/functions3D/CoherenceFilterStep3D.m",454 "sha256": "508ed1b472e87343b54992421c5b45c3cfbab5507da9ec0ea235041eeeb04039",455 "language": "MATLAB",456 "lines": 16,457 "truncated": false,458 "block": 14,459 "row": 18913460 },461 {462 "path": "functions/coherencefilter_version5b/functions3D/CoherenceFilterStep3D_functions.c",463 "sha256": "4e7cf77aad0f136dd3abf7c1c13fdf9c3e8653266dbf44995f5457a755b985a9",464 "language": "C",465 "lines": 1214,466 "truncated": false,467 "block": 14,468 "row": 601469 },470 {471 "path": "functions/coherencefilter_version5b/functions3D/EigenDecomposition3.c",472 "sha256": "ef9cca74794f4b0c514064b19915c439afb9ae5feede247acc8566b1b1cde71e",473 "language": "C",474 "lines": 351,475 "truncated": false,476 "block": 14,477 "row": 381478 },479 {480 "path": "functions/coherencefilter_version5b/functions3D/EigenDecomposition3.h",481 "sha256": "581405cd0ea5e2872a6b9a3bb642ef04c27c4c954a549224c7d8799c5e2cc005",482 "language": "C/C++",483 "lines": 4,484 "truncated": false,485 "block": 14,486 "row": 3580487 },488 {489 "path": "functions/coherencefilter_version5b/functions3D/EigenVectors3D.c",490 "sha256": "900f91852892f2caaf57f1a45f9b0f4936402388073f09ba3b4acaf4654b8009",491 "language": "C",492 "lines": 90,493 "truncated": false,494 "block": 14,495 "row": 144496 },497 {498 "path": "functions/coherencefilter_version5b/functions3D/EigenVectors3D.m",499 "sha256": "de090e4b8813c19b010a433ecdf5a790e05d92dfc35b33c78025322005c8bd42",500 "language": "MATLAB",501 "lines": 45,502 "truncated": false,503 "block": 14,504 "row": 21446505 },506 {507 "path": "functions/coherencefilter_version5b/functions3D/StructureTensor2DiffusionTensor3D.c",508 "sha256": "0850944bdf528f586dc58653ef9adf5f2e20225b488b50241f624e9fdbc3f04a",509 "language": "C",510 "lines": 462,511 "truncated": false,512 "block": 14,513 "row": 474514 },515 {516 "path": "functions/coherencefilter_version5b/functions3D/StructureTensor2DiffusionTensor3D.m",517 "sha256": "fb2f439606adfe17bb593c069732ffaa98603af130ab0b1fedf5d481d0e409b6",518 "language": "MATLAB",519 "lines": 69,520 "truncated": false,521 "block": 14,522 "row": 24764523 },524 {525 "path": "functions/coherencefilter_version5b/functions3D/StructureTensor3D.m",526 "sha256": "09059b6c17f7448f8e6f53c30f7ad2fc407b199cd3737dae07ddf09c69615e47",527 "language": "MATLAB",528 "lines": 21,529 "truncated": false,530 "block": 14,531 "row": 18819532 },533 {534 "path": "functions/coherencefilter_version5b/functions3D/diffusion_scheme_3D_implicit.m",535 "sha256": "64f31a3f12c9976d6cf3aa42124b35911c3d70f85190a9230f115da13a3ca09e",536 "language": "MATLAB",537 "lines": 77,538 "truncated": false,539 "block": 14,540 "row": 24943541 },542 {543 "path": "functions/coherencefilter_version5b/functions3D/diffusion_scheme_3D_non_negativity.c",544 "sha256": "5f24cf86f9ede4ae53b218929b2ba4377daaa8dbffcc52d5b4ee0d1b42e33312",545 "language": "C",546 "lines": 185,547 "truncated": false,548 "block": 14,549 "row": 319550 },551 {552 "path": "functions/coherencefilter_version5b/functions3D/diffusion_scheme_3D_non_negativity.m",553 "sha256": "de2fb04f11475d06991432765d3116ca3221b390a1f75d52efdfb8496f5be230",554 "language": "MATLAB",555 "lines": 74,556 "truncated": false,557 "block": 14,558 "row": 24867559 },560 {561 "path": "functions/coherencefilter_version5b/functions3D/diffusion_scheme_3D_novel.m",562 "sha256": "2759b5db71acf706af58b640501decab7e2a0fbbd544804819ae94bbabc35ddd",563 "language": "MATLAB",564 "lines": 57,565 "truncated": false,566 "block": 14,567 "row": 24117568 },569 {570 "path": "functions/coherencefilter_version5b/functions3D/diffusion_scheme_3D_novel_getUpdate.c",571 "sha256": "657532d8a0c703365d1e84839f32f313d0208eddc42890e663fd7508a0d2c610",572 "language": "C",573 "lines": 129,574 "truncated": false,575 "block": 14,576 "row": 207577 },578 {579 "path": "functions/coherencefilter_version5b/functions3D/diffusion_scheme_3D_novel_getUpdate.m",580 "sha256": "bde2ea7aa05ce1376b70929c243050f8b6b4137f7ef3fc39eec0d1b9c1c97ef8",581 "language": "MATLAB",582 "lines": 30,583 "truncated": false,584 "block": 14,585 "row": 20922586 },587 {588 "path": "functions/coherencefilter_version5b/functions3D/diffusion_scheme_3D_rotation_invariant.c",589 "sha256": "89c7c1b64579575afd4c44c3d4d1d8e71d2566fe6cea068d2b8126e0333d090a",590 "language": "C",591 "lines": 402,592 "truncated": false,593 "block": 14,594 "row": 435595 },596 {597 "path": "functions/coherencefilter_version5b/functions3D/diffusion_scheme_3D_rotation_invariant.m",598 "sha256": "eab99ba4a3037241c964b052950e4264ffeb1450a03a93391931099d70ea6247",599 "language": "MATLAB",600 "lines": 30,601 "truncated": false,602 "block": 14,603 "row": 20565604 },605 {606 "path": "functions/coherencefilter_version5b/functions3D/diffusion_scheme_3D_standard.c",607 "sha256": "75a62196732b8e00de042359629c5fc59bfa9c30f0c594303b0bbbd50fb426a1",608 "language": "C",609 "lines": 151,610 "truncated": false,611 "block": 14,612 "row": 256613 },614 {615 "path": "functions/coherencefilter_version5b/functions3D/diffusion_scheme_3D_standard.m",616 "sha256": "103b972ef75e293b01383631dfe96d5fab391f2b4f3ec810aac0af52e75b276e",617 "language": "MATLAB",618 "lines": 82,619 "truncated": false,620 "block": 14,621 "row": 23923622 },623 {624 "path": "functions/coherencefilter_version5b/optimization/error_diffusion_scheme_2D.m",625 "sha256": "29fb6b95f696cdfd99697a08d97597b9b2025ae24c55426ddb485aefc83fcc9e",626 "language": "MATLAB",627 "lines": 31,628 "truncated": false,629 "block": 14,630 "row": 19848631 },632 {633 "path": "functions/coherencefilter_version5b/optimization/error_diffusion_scheme_3D.m",634 "sha256": "16ef3ffa8520d8f389c187bcbc7ed852fcb24ee586544bf8d40ed819106a3e85",635 "language": "MATLAB",636 "lines": 30,637 "truncated": false,638 "block": 14,639 "row": 20086640 },641 {642 "path": "functions/coherencefilter_version5b/optimization/fitgaussian.m",643 "sha256": "b1223f8068eded430f83ab96a6f70202295474b22d0092af5069fda036113dd2",644 "language": "MATLAB",645 "lines": 12,646 "truncated": false,647 "block": 14,648 "row": 18001649 },650 {651 "path": "functions/coherencefilter_version5b/optimization/fminlbfgs.m",652 "sha256": "865f7db2121f70480b7aea30c9ddd6f45d2be45361c2a1d51d8b5de5d198c09f",653 "language": "MATLAB",654 "lines": 829,655 "truncated": false,656 "block": 15,657 "row": 4599658 },659 {660 "path": "functions/coherencefilter_version5b/optimization/optimize_scheme_2D.m",661 "sha256": "9420e6f012e7323dca82e34043f592e50afb5981ada0cabe1a6e8425df8cd05f",662 "language": "MATLAB",663 "lines": 67,664 "truncated": false,665 "block": 14,666 "row": 23855667 },668 {669 "path": "functions/coherencefilter_version5b/optimization/optimize_scheme_3D.m",670 "sha256": "fed53cc184a72ba6ad36254f6b3ec95e93f5ff63b3536076c6a6c4b3e5f4b372",671 "language": "MATLAB",672 "lines": 73,673 "truncated": false,674 "block": 14,675 "row": 24404676 },677 {678 "path": "functions/combineFOV.m",679 "sha256": "921c00e2ee737d2d7eb236d0dd3c86af696ce252777ed98f542196c850dd490e",680 "language": "MATLAB",681 "lines": 286,682 "truncated": false,683 "block": 15,684 "row": 3356685 },686 {687 "path": "functions/combineStrings.m",688 "sha256": "4b71419984ac3dbef397282159249d335f3efa6fcab96fc09d37eac9f127bd10",689 "language": "MATLAB",690 "lines": 37,691 "truncated": false,692 "block": 14,693 "row": 20692694 },695 {696 "path": "functions/compareFileNumbers.m",697 "sha256": "756299c70eb2d39968ba7abb52284e56982866bed3c0241da3958e31992e0629",698 "language": "MATLAB",699 "lines": 124,700 "truncated": false,701 "block": 15,702 "row": 472703 },704 {705 "path": "functions/computeImageGradient.m",706 "sha256": "c443ddc79f4941d03d99134ab4c5bdf84a95ab5d251f465aae7ac4bbf2e16cea",707 "language": "MATLAB",708 "lines": 59,709 "truncated": false,710 "block": 14,711 "row": 22655712 },713 {714 "path": "functions/concatCells.m",715 "sha256": "1185639c7e8d468902c42e752bb566827846f3d37b7769ed978c627b1c70473e",716 "language": "MATLAB",717 "lines": 86,718 "truncated": false,719 "block": 14,720 "row": 23847721 },722 {723 "path": "functions/continuous_zline_detection/Tests/addExperimentalTestCase.m",724 "sha256": "0a1f91f72f5992de7a672209b8485a5bfeadb7c11071fb0c75025f9e62647cd8",725 "language": "MATLAB",726 "lines": 61,727 "truncated": false,728 "block": 14,729 "row": 22689730 },731 {732 "path": "functions/continuous_zline_detection/Tests/createTestCases.m",733 "sha256": "a0e9375eaae4f0a6979ac2446491ea804c9443dc06cdef8d8092a1d946288d6f",734 "language": "MATLAB",735 "lines": 386,736 "truncated": false,737 "block": 15,738 "row": 3140739 },740 {741 "path": "functions/continuous_zline_detection/Tests/runExperimentalTestCases.m",742 "sha256": "7797fc29d0cfc245068881c0f7447fb686de07a635ae539a518edd486e866e08",743 "language": "MATLAB",744 "lines": 137,745 "truncated": false,746 "block": 15,747 "row": 739748 },749 {750 "path": "functions/continuous_zline_detection/Tests/testExperimental.m",751 "sha256": "c151c25c2ef4df02dc5e5d9c3217d0c28139adca64012f4c9727fee7afb6b7e3",752 "language": "MATLAB",753 "lines": 218,754 "truncated": false,755 "block": 15,756 "row": 2073757 },758 {759 "path": "functions/continuous_zline_detection/Tests/testSynthetic.m",760 "sha256": "64a87ce729ce8fa850ec189b735a34a9665bc349fb71a38fa3a6bafbf77fd9e9",761 "language": "MATLAB",762 "lines": 140,763 "truncated": false,764 "block": 15,765 "row": 800766 },767 {768 "path": "functions/continuous_zline_detection/add_to_cluster.m",769 "sha256": "b4e6995ddbdb5c40673faf8361ef768e6c5091f624cac0e1a9bd7d2102d8e6ea",770 "language": "MATLAB",771 "lines": 210,772 "truncated": false,773 "block": 15,774 "row": 2330775 },776 {777 "path": "functions/continuous_zline_detection/all_max.m",778 "sha256": "e14066ff1f3eff541a52b99e2e36311f32d4184a6a2e2d7e18446303b56ae2e8",779 "language": "MATLAB",780 "lines": 35,781 "truncated": false,782 "block": 14,783 "row": 20383784 },785 {786 "path": "functions/continuous_zline_detection/appendFilename.m",787 "sha256": "f5b36a7dd41748eb4cb6a9a302b915f7006dacfe615e0c43fea38e6b781187f0",788 "language": "MATLAB",789 "lines": 61,790 "truncated": false,791 "block": 14,792 "row": 21884793 },794 {795 "path": "functions/continuous_zline_detection/boundary_correction.m",796 "sha256": "92dcf10f5f9ca66e66b31f420ea51b217b7608217dc7eb7e2351529891b94fc8",797 "language": "MATLAB",798 "lines": 27,799 "truncated": false,800 "block": 14,801 "row": 20514802 },803 {804 "path": "functions/continuous_zline_detection/calculate_lengths.m",805 "sha256": "b8624fc9c979a587088cfff63ef35007689df332fee70df1f49c7e252c40bdaf",806 "language": "MATLAB",807 "lines": 78,808 "truncated": false,809 "block": 14,810 "row": 23068811 },812 {813 "path": "functions/continuous_zline_detection/checkDistantNeighbor.m",814 "sha256": "9253ef0fab63a0d7e27b1c2f2483ce1c158995563a8d748f40aae35de309044d",815 "language": "MATLAB",816 "lines": 174,817 "truncated": false,818 "block": 15,819 "row": 1876820 },821 {822 "path": "functions/continuous_zline_detection/check_perpendicular.m",823 "sha256": "1c1597888d3a296a3e9b5f03185c263d8ce3fba198d511cd7a82a9a0eaed4a8e",824 "language": "MATLAB",825 "lines": 45,826 "truncated": false,827 "block": 14,828 "row": 21177829 },830 {831 "path": "functions/continuous_zline_detection/cluster_neighbors.m",832 "sha256": "010b46b8fd119dc044a50b44cd889ffa4c7019ac25b0d416363c80fa0baa8d18",833 "language": "MATLAB",834 "lines": 307,835 "truncated": false,836 "block": 15,837 "row": 3585838 },839 {840 "path": "functions/continuous_zline_detection/combine_clusters.m",841 "sha256": "f6874aa447b9881bc3631545fe159df723cdb39fa655282d6ffb77a44152819c",842 "language": "MATLAB",843 "lines": 203,844 "truncated": false,845 "block": 15,846 "row": 2447847 },848 {849 "path": "functions/continuous_zline_detection/compare_angles.m",850 "sha256": "7aecfd3f2d21e9efb47c8f68baca4b2252ba5701b6b017ad8378c71ef4c2286c",851 "language": "MATLAB",852 "lines": 163,853 "truncated": false,854 "block": 15,855 "row": 1696856 },857 {858 "path": "functions/continuous_zline_detection/connectivity_8_neighbors.m",859 "sha256": "f4288d2ece7df7af69e0ee0a49a5c4258f4a5c46837366eddf6f290b5ef21a20",860 "language": "MATLAB",861 "lines": 59,862 "truncated": false,863 "block": 14,864 "row": 22723865 },866 {867 "path": "functions/continuous_zline_detection/continuous_zline_detection.m",868 "sha256": "a62429247adfe450684db6c2699bd7366e4ab49c86aadc9c9a023e61707af6f9",869 "language": "MATLAB",870 "lines": 173,871 "truncated": false,872 "block": 15,873 "row": 2003874 },875 {876 "path": "functions/continuous_zline_detection/coordinatePosition.m",877 "sha256": "1ca557a26619a5246a7dee02237a93af3b8f04b5b217763d6494332c2930d177",878 "language": "MATLAB",879 "lines": 46,880 "truncated": false,881 "block": 14,882 "row": 21134883 },884 {885 "path": "functions/continuous_zline_detection/coordinate_distances.m",886 "sha256": "13fbeebf46106a130936e71e9ef9e192f576174852bf064d6de4d80973d86eb7",887 "language": "MATLAB",888 "lines": 35,889 "truncated": false,890 "block": 14,891 "row": 20870892 },893 {894 "path": "functions/continuous_zline_detection/create_cluster.m",895 "sha256": "722fd1568930863c372308a4b0cafebc09db0125a40554e35c93c8562445c984",896 "language": "MATLAB",897 "lines": 24,898 "truncated": false,899 "block": 14,900 "row": 19272901 },902 {903 "path": "functions/continuous_zline_detection/determine_case.m",904 "sha256": "bd4109295a972b9066bdbdd545e696dfadc831ca191a9cbc5e85d282e3b5035a",905 "language": "MATLAB",906 "lines": 185,907 "truncated": false,908 "block": 15,909 "row": 1994910 },911 {912 "path": "functions/continuous_zline_detection/find_angle_neighbors.m",913 "sha256": "c02d4fcb6f2a71df62609d3609f7b20e8ae4b4447eaa616df79bb564ca9a4ec4",914 "language": "MATLAB",915 "lines": 45,916 "truncated": false,917 "block": 14,918 "row": 21799919 },920 {921 "path": "functions/continuous_zline_detection/find_neighbor_connectivity.m",922 "sha256": "f22fa2dac0617e2d58930633dec0cfc83796df688abdb48f57778be30320d149",923 "language": "MATLAB",924 "lines": 83,925 "truncated": false,926 "block": 14,927 "row": 24582928 },929 {930 "path": "functions/continuous_zline_detection/get_assigner.m",931 "sha256": "28adf9d4105bad82c3929e2f69bf1a2c09d3aaed74292a8c67928183699bc279",932 "language": "MATLAB",933 "lines": 32,934 "truncated": false,935 "block": 14,936 "row": 19337937 },938 {939 "path": "functions/continuous_zline_detection/get_statistics.m",940 "sha256": "3d1216ef23c942f6073321a79da868d6718ec933fe25cee657e3d5c999436fb9",941 "language": "MATLAB",942 "lines": 22,943 "truncated": false,944 "block": 14,945 "row": 19218946 },947 {948 "path": "functions/continuous_zline_detection/get_values.m",949 "sha256": "c258a27cc69b1eac62596518cd60ef53a1c577ef1054f956b169a1f14120b6da",950 "language": "MATLAB",951 "lines": 30,952 "truncated": false,953 "block": 14,954 "row": 20289955 },956 {957 "path": "functions/continuous_zline_detection/neighborReciprocity.m",958 "sha256": "50b9f4f78cbfe84458075294e98ddd25a1f0ecc290fd25d6a8930220e33c662e",959 "language": "MATLAB",960 "lines": 87,961 "truncated": false,962 "block": 14,963 "row": 24991964 },965 {966 "path": "functions/continuous_zline_detection/neighbor_positions.m",967 "sha256": "ef4ebb4932a47e8b587322a688cf50354b44fdd82bf8e0074a1341e2c8b7477a",968 "language": "MATLAB",969 "lines": 85,970 "truncated": false,971 "block": 14,972 "row": 24135973 },974 {975 "path": "functions/continuous_zline_detection/orientimperp2orientim.m",976 "sha256": "ffd0258ca68d949557b161b32e03a381626fbd9455ff1e4b9be822362f9e7d03",977 "language": "MATLAB",978 "lines": 13,979 "truncated": false,980 "block": 14,981 "row": 18376982 },983 {984 "path": "functions/continuous_zline_detection/update_tracker.m",985 "sha256": "3d144c029bcfdce14bd7965ce27fe0c807e48aa7952c281aae127f5578e66c5c",986 "language": "MATLAB",987 "lines": 21,988 "truncated": false,989 "block": 14,990 "row": 19020991 },992 {993 "path": "functions/convertParameters.m",994 "sha256": "988181908e7a45a7057e7f78193f0ef3443ada62f5fac80caeda9d3edf8b196d",995 "language": "MATLAB",996 "lines": 54,997 "truncated": false,998 "block": 14,999 "row": 221301000 },1001 {1002 "path": "functions/createInitialMask.m",1003 "sha256": "68d5462570a51d182adfd4d78f3010089d5192f9d1f417ceedb4f2a283fbcd50",1004 "language": "MATLAB",1005 "lines": 49,1006 "truncated": false,1007 "block": 14,1008 "row": 219041009 },1010 {1011 "path": "functions/createSummaries.m",1012 "sha256": "dae4324988ea6c05bb5b06136baad8a238a49a37a65e0e78c70ba5b695980321",1013 "language": "MATLAB",1014 "lines": 588,1015 "truncated": false,1016 "block": 15,1017 "row": 44141018 },1019 {1020 "path": "functions/declareCondition.m",1021 "sha256": "88f063576137e9600dd1be93866ad672535854e90bca16046c4799360f9d9754",1022 "language": "MATLAB",1023 "lines": 80,1024 "truncated": false,1025 "block": 14,1026 "row": 234401027 },1028 {1029 "path": "functions/diffusionExploreImage.m",1030 "sha256": "451fa391376fc6c654aafab0b21a79e2951ebfcfca98ba06ed477dce17694a2d",1031 "language": "MATLAB",1032 "lines": 213,1033 "truncated": false,1034 "block": 15,1035 "row": 25941036 },1037 {1038 "path": "functions/diffusionParameterExploration.m",1039 "sha256": "73759dfb3900bdfd035f7e31560dbe7a9b5fa75127b2dee0f519f6d3a0ad8652",1040 "language": "MATLAB",1041 "lines": 142,1042 "truncated": false,1043 "block": 15,1044 "row": 13171045 },1046 {1047 "path": "functions/doStringComparison.m",1048 "sha256": "c3208a9011162c5d9b41f4a6f20f45c8dc66075c796b703e44e4529bb01acd8d",1049 "language": "MATLAB",1050 "lines": 25,1051 "truncated": false,1052 "block": 14,1053 "row": 185261054 },1055 {1056 "path": "functions/findNearBranch.m",1057 "sha256": "eb28e546de4490095ad6466fda87cd70f638a58a3659a7afbb933eda9c40b00d",1058 "language": "MATLAB",1059 "lines": 70,1060 "truncated": false,1061 "block": 14,1062 "row": 234731063 },1064 {1065 "path": "functions/getGUIsettings.m",1066 "sha256": "3ef132bd66d493cbbdb7670784662d1114d55d24a2c9cf63a502e46daca5d72b",1067 "language": "MATLAB",1068 "lines": 238,1069 "truncated": false,1070 "block": 15,1071 "row": 30401072 },1073 {1074 "path": "functions/getZlineDetectionImages.m",1075 "sha256": "eb117d1a1202a4feffcc94f53494753199e3bd727b3a509abfbd4b15c570f604",1076 "language": "MATLAB",1077 "lines": 216,1078 "truncated": false,1079 "block": 15,1080 "row": 27331081 },1082 {1083 "path": "functions/hog.m",1084 "sha256": "a4495bb7d732ab0d5283ce6cff432138e26fb3a307c55aa16648c4ef1019c61c",1085 "language": "MATLAB",1086 "lines": 161,1087 "truncated": false,1088 "block": 15,1089 "row": 18211090 },1091 {1092 "path": "functions/insertSegment.m",1093 "sha256": "e51ec91312bec2b4dc06d2f6a126d3c26c12fab21da773997e9c8aaaab481ab9",1094 "language": "MATLAB",1095 "lines": 37,1096 "truncated": false,1097 "block": 14,1098 "row": 196121099 },1100 {1101 "path": "functions/labelSkeleton.m",1102 "sha256": "f05280948fc1053f65a94e33f46a20809f4bda50278ab6239bfcbf73fa6ad226",1103 "language": "MATLAB",1104 "lines": 44,1105 "truncated": false,1106 "block": 14,1107 "row": 206671108 },1109 {1110 "path": "functions/load_files.m",1111 "sha256": "844f0282d002c1aeebee0f48669d95313dced7952b9f38ece1aa32aa4a65233c",1112 "language": "MATLAB",1113 "lines": 71,1114 "truncated": false,1115 "block": 14,1116 "row": 227131117 },1118 {1119 "path": "functions/makeGray.m",1120 "sha256": "50d2ad19d51a2cc7059f493a60484c3fb2a5332ec224ec8633903df2ebe1f59c",1121 "language": "MATLAB",1122 "lines": 37,1123 "truncated": false,1124 "block": 14,1125 "row": 196041126 },1127 {1128 "path": "functions/modifyROI.m",1129 "sha256": "03ecc3976b969c5ef8a2640cd2bae71956a79b31fd1bf5628abcf633d6be698e",1130 "language": "MATLAB",1131 "lines": 114,1132 "truncated": false,1133 "block": 15,1134 "row": 2101135 },1136 {1137 "path": "functions/normalise.m",1138 "sha256": "b2f13155183c4691c597586ee75586b7e39e78d0043e3fbb1e5be31b320c32cc",1139 "language": "MATLAB",1140 "lines": 70,1141 "truncated": false,1142 "block": 14,1143 "row": 234241144 },1145 {1146 "path": "functions/orientInfo.m",1147 "sha256": "5f38d3c96f2f0952b744baf9b0b47974a02063f1a591613c7d74c0040266f4fb",1148 "language": "MATLAB",1149 "lines": 51,1150 "truncated": false,1151 "block": 14,1152 "row": 220161153 },1154 {1155 "path": "functions/parameterExploreAnalyzeImage.m",1156 "sha256": "0f25f64842f3d335fcbf21c2caf7210015cadbc42b92bf412e8c883fe191711c",1157 "language": "MATLAB",1158 "lines": 237,1159 "truncated": false,1160 "block": 15,1161 "row": 27001162 },1163 {1164 "path": "functions/plotCSresults.m",1165 "sha256": "cde4295e7ae5b9a1f02a82899e02164f701b6429418d43a34ae9c32f82d93f5a",1166 "language": "MATLAB",1167 "lines": 474,1168 "truncated": false,1169 "block": 15,1170 "row": 38451171 },1172 {1173 "path": "functions/plotConditions.m",1174 "sha256": "9a6afd5ff5fe964e19721186590aeae67c22f4fdd3465134c06eda2180530585",1175 "language": "MATLAB",1176 "lines": 528,1177 "truncated": false,1178 "block": 15,1179 "row": 41221180 },1181 {1182 "path": "functions/plotSLhist.m",1183 "sha256": "0cf66238fca522d97af6d70aab22a43ff044029a1e8218ccfd628a0c8139bbaf",1184 "language": "MATLAB",1185 "lines": 46,1186 "truncated": false,1187 "block": 14,1188 "row": 213551189 },1190 {1191 "path": "functions/plotSarcLengthIM.m",1192 "sha256": "cadb215e424d05ef2cc815f22d8d6f94451dc233251297f16fb6e13d3cda113e",1193 "language": "MATLAB",1194 "lines": 36,1195 "truncated": false,1196 "block": 14,1197 "row": 199851198 },1199 {1200 "path": "functions/plottingFunctions/boxPlot.m",