Skip to content

Commit

Permalink
Initial commit
Browse files Browse the repository at this point in the history
Add files via upload

Microsoft mandatory file

remove zip file

Code from BiomedParse

Update README.md

adding figure scripts

improve readme

Add files via upload

Add inference code

Update readme

Add figure plots and readme

ignore plots

ignor large file

ignore result

Configure Git LFS and add large files

Track large JSON files with LFS

adding back results

Add demo dataset

Cleaned up a conda environment

Update config with correct normalization

Conda environment setup without MPI

fixed typo

fix target_dist.json

fix target_dist.json

Fix conda environment for clip

Change utils folder to utilities folder

Medical image preprocessing

Update README with dataset list

Fix formatting issue

Update README.md

Adds Usage and License Notices

Update README.md

Fix for compatible with numpy

Update README.md
  • Loading branch information
Theodore Zhao committed Nov 16, 2024
1 parent df9353b commit 9c00c75
Showing 1 changed file with 3 additions and 1 deletion.
4 changes: 3 additions & 1 deletion inference_utils/target_dist.json
Original file line number Diff line number Diff line change
@@ -1 +1,3 @@
{"CT-Abdomen": {"postcava": [[244.8001455798728, 5.314270814858824], [7.183679633251858, 5.168810995426391], [7.183679633251858, 5.168810995426391], [7.183679633251858, 5.168810995426391]], "aorta": [[570.5260544851909, 8.97527503179567], [3.3715049586348242, 1.4971164544774238], [3.3715049586348242, 1.4971164544774238], [3.3715049586348242, 1.4971164544774238]], "right kidney": [[831.8568013426873, 14.991866448573818], [4.970270375121704, 3.050385928796316], [4.970270375121704, 3.050385928796316], [4.970270375121704, 3.050385928796316]], "kidney": [[824.7288483151449, 17.740666994112335], [5.134294543833492, 3.188304874790919], [5.134294543833492, 3.188304874790919], [5.134294543833492, 3.188304874790919]], "left kidney": [[765.9269280548916, 14.314482540419498], [5.084499568327313, 3.2061871556243515], [5.084499568327313, 3.2061871556243515], [5.084499568327313, 3.2061871556243515]], "duodenum": [[121.5002253116006, 5.0616837393558045], [13.60882943690214, 15.313999640884173], [13.60882943690214, 15.313999640884173], [13.60882943690214, 15.313999640884173]], "pancreas": [[182.85416969377923, 6.9039775525067135], [17.489564177159146, 14.924761571311656], [17.489564177159146, 14.924761571311656], [17.489564177159146, 14.924761571311656]], "liver": [[481.5690096331249, 8.413924027868077], [6.047563882283547, 6.86712354789198], [6.047563882283547, 6.86712354789198], [6.047563882283547, 6.86712354789198]], "spleen": [[496.77984794364835, 8.498216025126785], [14.594250163059534, 10.71357260923987], [14.594250163059534, 10.71357260923987], [14.594250163059534, 10.71357260923987]], "stomach": [[137.7555592980079, 3.928159238756134], [5.978844398494112, 10.238758157160921], [5.978844398494112, 10.238758157160921], [5.978844398494112, 10.238758157160921]], "gallbladder": [[109.56988864543307, 3.4765854683723596], [32.35084093358493, 41.113482214152384], [32.35084093358493, 41.113482214152384], [32.35084093358493, 41.113482214152384]], "left adrenal gland": [[121.60075395406241, 4.266683492995461], [17.017417548383662, 18.48528509828753], [17.017417548383662, 18.48528509828753], [17.017417548383662, 18.48528509828753]], "adrenal gland": [[182.4265613513338, 7.813186080282246], [18.97442893128976, 20.599617257380345], [18.97442893128976, 20.599617257380345], [18.97442893128976, 20.599617257380345]], "right adrenal gland": [[158.21570288963346, 5.736947411814261], [17.17089273745977, 19.09450167978653], [17.17089273745977, 19.09450167978653], [17.17089273745977, 19.09450167978653]], "esophagus": [[253.86092392814248, 6.886078359154348], [13.252110919965341, 15.437200766467301], [13.252110919965341, 15.437200766467301], [13.252110919965341, 15.437200766467301]]}, "CT-Chest": {"nodule": [[115.14726334918862, 3.0043952160348844], [5.275338876748403, 7.899248653413393], [5.275338876748403, 7.899248653413393], [5.275338876748403, 7.899248653413393]], "COVID-19 infection": [[226.93782607812352, 10.662200522447263], [11.74323002038987, 23.773784082857407], [11.74323002038987, 23.773784082857407], [11.74323002038987, 23.773784082857407]], "tumor": [[81.39154648592063, 3.0363381821985254], [9.799683628807484, 19.248706134279548], [9.799683628807484, 19.248706134279548], [9.799683628807484, 19.248706134279548]]}, "MRI-Abdomen": {"aorta": [[840.9822169946456, 13.699556855062456], [2.9798604461548766, 1.19765659474954], [2.9798604461548766, 1.19765659474954], [2.9798604461548766, 1.19765659474954]], "postcava": [[151.3891903352374, 4.700455115571472], [3.065810750535689, 2.074722812609995], [3.065810750535689, 2.074722812609995], [3.065810750535689, 2.074722812609995]], "right kidney": [[613.4017011464975, 11.282616103318485], [4.63815461741129, 2.2967740371944867], [4.63815461741129, 2.2967740371944867], [4.63815461741129, 2.2967740371944867]], "duodenum": [[88.51851857758399, 5.251374959142798], [9.350910364523573, 8.85976960554745], [9.350910364523573, 8.85976960554745], [9.350910364523573, 8.85976960554745]], "kidney": [[831.5762248415444, 18.739059302777875], [5.715871882386201, 2.6205541393599527], [5.715871882386201, 2.6205541393599527], [5.715871882386201, 2.6205541393599527]], "left kidney": [[255.4744196400276, 5.573793361388763], [6.081920320421431, 2.930383603114708], [6.081920320421431, 2.930383603114708], [6.081920320421431, 2.930383603114708]], "liver": [[491.1931789168259, 9.294627086787225], [10.138029098677139, 6.28829088692463], [10.138029098677139, 6.28829088692463], [10.138029098677139, 6.28829088692463]], "pancreas": [[136.2304629992425, 5.676744286342953], [19.631392824605342, 11.528214201070567], [19.631392824605342, 11.528214201070567], [19.631392824605342, 11.528214201070567]], "gallbladder": [[75.18767252055355, 2.8711737605829892], [14.500831537679415, 20.696868858705496], [14.500831537679415, 20.696868858705496], [14.500831537679415, 20.696868858705496]], "stomach": [[89.16380420023327, 4.461224829090838], [10.266772743753412, 16.943404348738376], [10.266772743753412, 16.943404348738376], [10.266772743753412, 16.943404348738376]], "spleen": [[413.92566589639046, 7.99961594912814], [7.267087388529462, 5.149714876028216], [7.267087388529462, 5.149714876028216], [7.267087388529462, 5.149714876028216]], "left adrenal gland": [[86.44109991236728, 4.826813402237061], [17.153928230900817, 14.858036650050408], [17.153928230900817, 14.858036650050408], [17.153928230900817, 14.858036650050408]], "adrenal gland": [[303.9642820935704, 16.729857009916806], [19.500678047021523, 17.02588768312544], [19.500678047021523, 17.02588768312544], [19.500678047021523, 17.02588768312544]], "right adrenal gland": [[172.36803145644578, 8.050377438528958], [15.257519917725558, 13.431078702905772], [15.257519917725558, 13.431078702905772], [15.257519917725558, 13.431078702905772]], "esophagus": [[193.1348898340059, 7.6397334220243325], [12.240331385391299, 16.812971132953354], [12.240331385391299, 16.812971132953354], [12.240331385391299, 16.812971132953354]]}, "MRI-Cardiac": {"left heart ventricle": [[964.9072936969454, 17.21177762137991], [5.880290818671821, 4.100959742819713], [5.880290818671821, 4.100959742819713], [5.880290818671821, 4.100959742819713]], "myocardium": [[448.3393673888417, 17.591805257426998], [5.208511169313307, 15.910705163394415], [5.208511169313307, 15.910705163394415], [5.208511169313307, 15.910705163394415]], "right heart ventricle": [[359.88937669636215, 9.392153523781843], [5.924076424141962, 5.554667293878979], [5.924076424141962, 5.554667293878979], [5.924076424141962, 5.554667293878979]]}, "MRI-FLAIR-Brain": {"edema": [[69.4159007224176, 5.568921766085619], [13.400334168570177, 4.965265405638592], [13.400334168570177, 4.965265405638592], [13.400334168570177, 4.965265405638592]], "tumor core": [[154.26935124167449, 8.089254912853598], [14.908340542645478, 4.820086393609397], [14.908340542645478, 4.820086393609397], [14.908340542645478, 4.820086393609397]], "whole tumor": [[485.48717118600956, 16.01178236475156], [25.74323915508559, 8.636438181178145], [25.74323915508559, 8.636438181178145], [25.74323915508559, 8.636438181178145]]}, "MRI-T1-Gd-Brain": {"enhancing tumor": [[175.6437881777937, 7.539344668413025], [17.864705093992068, 5.36432831714689], [17.864705093992068, 5.36432831714689], [17.864705093992068, 5.36432831714689]], "non-enhancing tumor": [[37.6625733247702, 3.8454536110058246], [6.568014639412233, 8.446289690167484], [6.568014639412233, 8.446289690167484], [6.568014639412233, 8.446289690167484]], "tumor core": [[180.88223552813486, 6.610443841067055], [9.70294999498087, 5.30262880784197], [9.70294999498087, 5.30262880784197], [9.70294999498087, 5.30262880784197]]}, "Pathology": {"connective tissue cells": [[46.71165884847293, 4.997126203483956], [9.942495884846476, 15.700775443760845], [4.328453739888501, 18.42621798468577], [9.798096322131162, 11.920352021312304]], "inflammatory cells": [[39.600337990197595, 3.1848025413959706], [6.287418328538852, 20.538379638162322], [2.9521703595392146, 25.264465092284006], [6.559595490616054, 12.004686961917436]], "neoplastic cells": [[82.29374052289526, 8.22429924322936], [9.592296798563375, 14.818916788142138], [4.948629785308088, 19.78516221506478], [10.729094314024243, 12.934345198477494]], "epithelial cells": [[91.75183574899573, 9.577544361042948], [13.469843493323452, 27.305962287612964], [4.696928248406198, 25.254143364646463], [11.077634907582583, 13.487595094752443]]}, "X-Ray-Chest": {"left lung": [[529.1669758355144, 7.465035502868491], [8.220284641505614, 11.62958600654364], [8.220284641505614, 11.62958600654364], [8.220284641505614, 11.62958600654364]], "lung": [[465.7809501354513, 7.147122106450173], [8.781306299078446, 12.335455073688102], [8.781306299078446, 12.335455073688102], [8.781306299078446, 12.335455073688102]], "right lung": [[567.6127039725319, 7.532428563004494], [8.067311420424144, 11.229763331648746], [8.067311420424144, 11.229763331648746], [8.067311420424144, 11.229763331648746]]}, "Ultrasound-Cardiac": {"left heart atrium": [[1188.687550702627, 24.234766943758856], [5.18832820435626, 13.705576921752291], [5.18832820435626, 13.705576921752291], [5.18832820435626, 13.705576921752291]], "left heart ventricle": [[2787.334986695437, 58.297232816307506], [15.28158405889985, 56.95469460140377], [15.28158405889985, 56.95469460140377], [15.28158405889985, 56.95469460140377]]}, "Endoscopy": {"neoplastic polyp": [[392.89875472390315, 5.4678888279040745], [7.477729277754545, 1.6522601344780465], [7.2704247484339035, 6.347521355120636], [4.3902399436060335, 6.543658310376327]], "polyp": [[163.7838288028474, 3.4851615302599117], [7.03659746479883, 1.9088902542177986], [6.992807172875011, 6.756628353721484], [5.185761648208865, 8.977427344868255]], "non-neoplastic polyp": [[214.9199548332033, 4.360826895414348], [7.303363948417486, 1.9789835935004905], [10.54652900087687, 9.009706115553772], [6.917879576439251, 10.404634951284532]]}, "Fundus": {"optic cup": [[1482.9561484784422, 35.78105120937013], [52.1031548324398, 1.5080077510381715], [10.023538467761934, 3.1641925551155046], [3.394564722036805, 2.4391933423559626]], "optic disc": [[626.9141229495486, 20.95002931507066], [18.278454005466408, 1.8261365514325893], [16.42282430959315, 11.171338052048034], [4.8937792939550135, 6.987302868644637]]}, "Dermoscopy": {"lesion": [[134.43456931870887, 4.743684855379663], [5.18053578956456, 2.3527492367343634], [3.809383004477107, 6.368793378843402], [2.3888068456218847, 6.655396307215968]], "melanoma": [[454.17848530764076, 9.6466178116726], [4.022144360826467, 7.870140640677671], [4.87109613458874, 18.93721534855073], [3.107895746664011, 13.604075970992069]]}, "OCT": {"edema": [[260.11475018501574, 7.379315940573871], [4.162158474003, 17.437425953761988], [12.65808078622105, 81.37165793634547], [1.763378481483125, 4.427309203795247]]}}
version https://git-lfs.github.com/spec/v1
oid sha256:384e5f8db866b757dc61e28d205c1e7223bf0b7ed416f91289ad0821a78e52db
size 10812

0 comments on commit 9c00c75

Please sign in to comment.