fidopt Interactive view

KonfAI segmentation app

A KonfAI segmentation app run through konfai-apps: the variant names an app of fideus-labs/fidopt-segmentation, or one of Valentin Boussot's apps where it lives; the app writes its own labels, matched with the dataset's structures by name.

SegmentationGPUversion fideus-labs/fidopt-segmentation (private on Hugging Face for now)every datasetApache-2.0

Run it

With its KonfAI app, at the benchmark's settings (the fidopt app repositories are private for now: a Hugging Face token with access opens them):

pip install konfai-apps
appCommand
TotalSegmentator (total), the authors' packageGet the appkonfai-apps infer fideus-labs/fidopt-segmentation:TotalSegmentator -i image.nii.gz -o out --gpu 0
TotalSegmentator (total), KonfAI appGet the appkonfai-apps infer VBoussot/TotalSegmentator-KonfAI:total -i image.nii.gz -o out --gpu 0
TotalSegmentator (total_mr), the authors' packageGet the appkonfai-apps infer fideus-labs/fidopt-segmentation:TotalSegmentator_MR -i image.nii.gz -o out --gpu 0
TotalSegmentator (total_mr), KonfAI appGet the appkonfai-apps infer VBoussot/TotalSegmentator-KonfAI:total_mr -i image.nii.gz -o out --gpu 0
IMPACTSeg body, KonfAI appGet the appkonfai-apps infer VBoussot/ImpactSeg:body -i image.nii.gz -o out --gpu 0
MRSegmentator, KonfAI appGet the appkonfai-apps infer VBoussot/MRSegmentator-KonfAI:MRSegmentator -i image.nii.gz -o out --gpu 0
DentalSegmentator, KonfAI appGet the appkonfai-apps infer VBoussot/DentalSegmentator-KonfAI:DentalSegmentator -i image.nii.gz -o out --gpu 0
TotalSegmentator (lung_vessels), the authors' packageGet the appkonfai-apps infer fideus-labs/fidopt-segmentation:TotalSegmentator_lung_vessels -i image.nii.gz -o out --gpu 0
TotalSegmentator (lung_nodules), the authors' packageGet the appkonfai-apps infer fideus-labs/fidopt-segmentation:TotalSegmentator_lung_nodules -i image.nii.gz -o out --gpu 0
TotalSegmentator (liver_vessels), the authors' packageGet the appkonfai-apps infer fideus-labs/fidopt-segmentation:TotalSegmentator_liver_vessels -i image.nii.gz -o out --gpu 0
TotalSegmentator (kidney_cysts), the authors' packageGet the appkonfai-apps infer fideus-labs/fidopt-segmentation:TotalSegmentator_kidney_cysts -i image.nii.gz -o out --gpu 0
TotalSegmentator (pleural_pericard_effusion), the authors' packageGet the appkonfai-apps infer fideus-labs/fidopt-segmentation:TotalSegmentator_pleural_pericard_effusion -i image.nii.gz -o out --gpu 0
TotalSegmentator (trunk_cavities), the authors' packageGet the appkonfai-apps infer fideus-labs/fidopt-segmentation:TotalSegmentator_trunk_cavities -i image.nii.gz -o out --gpu 0
TotalSegmentator (head_glands_cavities), the authors' packageGet the appkonfai-apps infer fideus-labs/fidopt-segmentation:TotalSegmentator_head_glands_cavities -i image.nii.gz -o out --gpu 0
TotalSegmentator (craniofacial_structures), the authors' packageGet the appkonfai-apps infer fideus-labs/fidopt-segmentation:TotalSegmentator_craniofacial_structures -i image.nii.gz -o out --gpu 0

Where it works

Its place on each kind of problem it has results on, among the methods ranked there. A method that leads one problem can trail another: read the one closest to yours.

ProblemappPlaceRankedDatasets
Abdomen CT, segmentationTotalSegmentator (total), KonfAI app1of 412 of 12
Body MR, many structures, segmentationTotalSegmentator (total_mr), the authors' package1of 41 of 1
Liver segmentation on CT without physical geometryTotalSegmentator (total), KonfAI app1of 51 of 1
Arterial liver MR, liver and hepatocellular carcinomaTotalSegmentator (total_mr), the authors' package1of 31 of 1
Clinical pelvic bones, CTPelvic1KTotalSegmentator (total), the authors' package1of 51 of 1
Simulated thoracic CBCT contoursIMPACTSeg body, KonfAI app1of 11 of 1
Abdomen CT, segmentationTotalSegmentator (total), the authors' package2of 412 of 12
Body MR, many structures, segmentationTotalSegmentator (total_mr), KonfAI app2of 41 of 1
Liver segmentation on CT without physical geometryTotalSegmentator (total), the authors' package2of 51 of 1
Arterial liver MR, liver and hepatocellular carcinomaTotalSegmentator (total_mr), KonfAI app2of 31 of 1
Clinical pelvic bones, CTPelvic1KTotalSegmentator (total), KonfAI app2of 51 of 1
Body MR, many structures, segmentationIMPACTSeg body, KonfAI app3of 41 of 1
Liver segmentation on CT without physical geometryMRSegmentator, KonfAI app3of 51 of 1
Arterial liver MR, liver and hepatocellular carcinomaMRSegmentator, KonfAI app3of 31 of 1
Abdomen CT, segmentationMRSegmentator, KonfAI app4of 412 of 12
Body MR, many structures, segmentationMRSegmentator, KonfAI app4of 41 of 1
Clinical pelvic bones, CTPelvic1KMRSegmentator, KonfAI app4of 51 of 1
Abdomen CT, segmentationTotalSegmentator (liver_vessels), the authors' packagenot ranked yet2 of 12
Abdomen CT, segmentationTotalSegmentator (kidney_cysts), the authors' packagenot ranked yet1 of 12
Body CT, many structures, segmentationIMPACTSeg body, KonfAI appnot ranked yet4 of 5
Body CT, many structures, segmentationTotalSegmentator (total), the authors' packagenot ranked yet4 of 5
Body CT, many structures, segmentationTotalSegmentator (total), KonfAI appnot ranked yet4 of 5
Body CT, many structures, segmentationMRSegmentator, KonfAI appnot ranked yet3 of 5
Body CT, many structures, segmentationTotalSegmentator (head_glands_cavities), the authors' packagenot ranked yet1 of 5
Body CT, many structures, segmentationTotalSegmentator (kidney_cysts), the authors' packagenot ranked yet1 of 5
Abdomen MR, segmentationMRSegmentator, KonfAI appnot ranked yet5 of 6
Abdomen MR, segmentationTotalSegmentator (total_mr), the authors' packagenot ranked yet4 of 6
Abdomen MR, segmentationTotalSegmentator (total_mr), KonfAI appnot ranked yet4 of 6
Abdomen MR, segmentationIMPACTSeg body, KonfAI appnot ranked yet1 of 6
Heart, segmentationMRSegmentator, KonfAI appnot ranked yet1 of 6
Heart, segmentationTotalSegmentator (total_mr), the authors' packagenot ranked yet1 of 6
Heart, segmentationTotalSegmentator (total_mr), KonfAI appnot ranked yet1 of 6
Chest CT, segmentationTotalSegmentator (lung_vessels), the authors' packagenot ranked yet2 of 4
Chest CT, segmentationIMPACTSeg body, KonfAI appnot ranked yet1 of 4
Chest CT, segmentationMRSegmentator, KonfAI appnot ranked yet1 of 4
Chest CT, segmentationTotalSegmentator (total), the authors' packagenot ranked yet1 of 4
Chest CT, segmentationTotalSegmentator (total), KonfAI appnot ranked yet1 of 4
Spine, bones and joints, segmentationTotalSegmentator (total), KonfAI appnot ranked yet4 of 9
Spine, bones and joints, segmentationTotalSegmentator (total), the authors' packagenot ranked yet3 of 9
Spine, bones and joints, segmentationIMPACTSeg body, KonfAI appnot ranked yet1 of 9
Spine, bones and joints, segmentationMRSegmentator, KonfAI appnot ranked yet1 of 9
Spine, bones and joints, segmentationTotalSegmentator (total_mr), the authors' packagenot ranked yet1 of 9
Spine, bones and joints, segmentationTotalSegmentator (total_mr), KonfAI appnot ranked yet1 of 9
Prostate and pelvis, segmentationTotalSegmentator (total), the authors' packagenot ranked yet1 of 6
Prostate and pelvis, segmentationTotalSegmentator (total), KonfAI appnot ranked yet1 of 6
Prostate and pelvis, segmentationTotalSegmentator (total_mr), the authors' packagenot ranked yet1 of 6
Prostate and pelvis, segmentationTotalSegmentator (total_mr), KonfAI appnot ranked yet1 of 6
Lesions and tumours, segmentationTotalSegmentator (lung_nodules), the authors' packagenot ranked yet2 of 33
Lesions and tumours, segmentationTotalSegmentator (liver_vessels), the authors' packagenot ranked yet1 of 33
Vessels, segmentationMRSegmentator, KonfAI appnot ranked yet1 of 2
Vessels, segmentationTotalSegmentator (total), the authors' packagenot ranked yet1 of 2
Vessels, segmentationTotalSegmentator (total), KonfAI appnot ranked yet1 of 2

Results

Datasetapp#Read byScoreFailedTime s
AMOS CT, abdominal organsTotalSegmentator (total), the authors' package1Dice0.7760142
AMOS CT, abdominal organsTotalSegmentator (total), KonfAI app2Dice0.766035
AMOS CT, abdominal organsMRSegmentator, KonfAI app5Dice0.219029
AMOS MR, abdominal organsTotalSegmentator (total_mr), KonfAI app1Dice0.72106
AMOS MR, abdominal organsTotalSegmentator (total_mr), the authors' package2Dice0.7180
AMOS MR, abdominal organsMRSegmentator, KonfAI app3Dice0.003014
ATM22TotalSegmentator (lung_vessels), the authors' package1Dice0.8620
AeroPathTotalSegmentator (lung_vessels), the authors' package1Dice0.8250
AVT aortic vessel treeTotalSegmentator (total), the authors' package1Dice0.8510
AVT aortic vessel treeTotalSegmentator (total), KonfAI app2Dice0.8490
AVT aortic vessel treeMRSegmentator, KonfAI app3Dice0.8500
MR enterography bowel segmentsTotalSegmentator (total_mr), KonfAI app1Dice0.414026
MR enterography bowel segmentsTotalSegmentator (total_mr), the authors' package2Dice0.4060
MR enterography bowel segmentsMRSegmentator, KonfAI app3Dice0.0341
CHAOS MR, liver, kidneys and spleenMRSegmentator, KonfAI app1Dice0.8900
CHAOS MR, liver, kidneys and spleenTotalSegmentator (total_mr), the authors' package2Dice0.8550
CHAOS MR, liver, kidneys and spleenTotalSegmentator (total_mr), KonfAI app3Dice0.847025
COVID-19 CT Lung and InfectionMRSegmentator, KonfAI app1Dice0.9040
COVID-19 CT Lung and InfectionTotalSegmentator (total), the authors' package2Dice0.8720
COVID-19 CT Lung and InfectionTotalSegmentator (total), KonfAI app3Dice0.859025
Colorectal-Liver-Metastases, liver and veinsTotalSegmentator (total), KonfAI app2Dice0.948020
Colorectal-Liver-Metastases, liver and veinsTotalSegmentator (total), the authors' package3Dice0.9480
Colorectal-Liver-Metastases, liver and veinsMRSegmentator, KonfAI app4Dice0.759222
CT-ORGTotalSegmentator (total), KonfAI app2Dice0.933022
CT-ORGTotalSegmentator (total), the authors' package3Dice0.9310
CT-ORGIMPACTSeg body, KonfAI app4Dice0.85906
CT-ORGMRSegmentator, KonfAI app7Dice0.6750
CTPelvic1K, CLINIC pelvic bonesTotalSegmentator (total), the authors' package1Dice0.9280
CTPelvic1K, CLINIC pelvic bonesTotalSegmentator (total), KonfAI app2Dice0.927028
CTPelvic1K, CLINIC pelvic bonesMRSegmentator, KonfAI app4Dice0.9020
FLARE22TotalSegmentator (total), the authors' package1Dice0.8910
FLARE22TotalSegmentator (total), KonfAI app2Dice0.890025
FLARE22MRSegmentator, KonfAI app5Dice0.0110
HCC-TACE-SegMRSegmentator, KonfAI app1Dice0.8380
HCC-TACE-SegTotalSegmentator (total), KonfAI app3Dice0.827018
HCC-TACE-SegTotalSegmentator (total), the authors' package4Dice0.8250
HCC-TACE-SegTotalSegmentator (liver_vessels), the authors' package5Dice0.514025
HQColon, colonTotalSegmentator (total), the authors' package1Dice0.8710
HQColon, colonTotalSegmentator (total), KonfAI app2Dice0.871020
HQColon, colonMRSegmentator, KonfAI app3Dice0.783162
HVSMR-2.0TotalSegmentator (total_mr), KonfAI app1Dice0.363025
HVSMR-2.0TotalSegmentator (total_mr), the authors' package2Dice0.329018
HVSMR-2.0MRSegmentator, KonfAI app3Dice0.0000
HaN-SegTotalSegmentator (craniofacial_structures), the authors' package1Dice0.943053
HaN-SegTotalSegmentator (head_glands_cavities), the authors' package2Dice0.644041
HaN-SegTotalSegmentator (total), the authors' package3Dice0.5990
HaN-SegTotalSegmentator (total), KonfAI app4Dice0.597058
HaN-SegIMPACTSeg body, KonfAI app6Dice0.198417
C4KC-KiTSMRSegmentator, KonfAI app1Dice0.8900
C4KC-KiTSTotalSegmentator (total), the authors' package2Dice0.8900
C4KC-KiTSTotalSegmentator (total), KonfAI app3Dice0.884025
T2-weighted Kidney MRITotalSegmentator (total_mr), KonfAI app1Dice0.876010
T2-weighted Kidney MRITotalSegmentator (total_mr), the authors' package2Dice0.867019
T2-weighted Kidney MRIMRSegmentator, KonfAI app3Dice0.2660
OAIZIB-CM, knee bones and cartilageTotalSegmentator (total_mr), KonfAI app1Dice0.926022
OAIZIB-CM, knee bones and cartilageTotalSegmentator (total_mr), the authors' package2Dice0.918022
OAIZIB-CM, knee bones and cartilageMRSegmentator, KonfAI app3Dice0.0000
Abdomen CT (Learn2Reg 2020, Task 3)MRSegmentator, KonfAI app1Dice0.3650
Abdomen CT (Learn2Reg 2020, Task 3)TotalSegmentator (total), the authors' package2Dice0.2640
Abdomen CT (Learn2Reg 2020, Task 3)TotalSegmentator (total), KonfAI app3Dice0.259023
Abdomen CT (Learn2Reg 2021, AbdomenMRCT)TotalSegmentator (total), the authors' package1Dice0.9020
Abdomen CT (Learn2Reg 2021, AbdomenMRCT)TotalSegmentator (total), KonfAI app2Dice0.90007
Abdomen CT (Learn2Reg 2021, AbdomenMRCT)MRSegmentator, KonfAI app4Dice0.0020
Abdomen MR (Learn2Reg 2021, AbdomenMRCT)TotalSegmentator (total_mr), the authors' package1Dice0.898039
Abdomen MR (Learn2Reg 2021, AbdomenMRCT)TotalSegmentator (total_mr), KonfAI app2Dice0.896011
Abdomen MR (Learn2Reg 2021, AbdomenMRCT)MRSegmentator, KonfAI app3Dice0.0000
LCTSC, thoracic organs at riskMRSegmentator, KonfAI app4Dice0.8570
LCTSC, thoracic organs at riskTotalSegmentator (total), the authors' package5Dice0.8350
LCTSC, thoracic organs at riskTotalSegmentator (total), KonfAI app6Dice0.835040
LCTSC, thoracic organs at riskIMPACTSeg body, KonfAI app7Dice0.7310
LNDbTotalSegmentator (lung_nodules), the authors' package1Dice0.2760
LiverHccSeg, arterial liver MRTotalSegmentator (total_mr), the authors' package1Dice0.898023
LiverHccSeg, arterial liver MRTotalSegmentator (total_mr), KonfAI app2Dice0.893027
LiverHccSeg, arterial liver MRMRSegmentator, KonfAI app3Dice0.0010
CT follow-up of liver metastases, liverMRSegmentator, KonfAI app1Dice0.7710
CT follow-up of liver metastases, liverTotalSegmentator (total), the authors' package4Dice0.0000
CT follow-up of liver metastases, liverTotalSegmentator (total), KonfAI app5Dice0.000014
PLC-CECT, delayed-phase liver segmentationTotalSegmentator (total), KonfAI app1Dice0.716026
PLC-CECT, delayed-phase liver segmentationTotalSegmentator (total), the authors' package2Dice0.6680
PLC-CECT, delayed-phase liver segmentationMRSegmentator, KonfAI app3Dice0.4061144
MSD LiverTotalSegmentator (total), KonfAI app1Dice0.921022
MSD LiverTotalSegmentator (total), the authors' package2Dice0.9200
MSD LiverTotalSegmentator (liver_vessels), the authors' package5Dice0.591042
MSD LiverMRSegmentator, KonfAI app6Dice0.006257
MSD PancreasTotalSegmentator (total), KonfAI app1Dice0.758026
MSD PancreasTotalSegmentator (total), the authors' package2Dice0.7580
MSD PancreasMRSegmentator, KonfAI app5Dice0.032122
MSD SpleenTotalSegmentator (total), KonfAI app1Dice0.943022
MSD SpleenTotalSegmentator (total), the authors' package2Dice0.9420
MSD SpleenMRSegmentator, KonfAI app5Dice0.0000
Spinal-Multiple-Myeloma-SEG, vertebrae and lytic lesionsTotalSegmentator (total), KonfAI app1Dice0.890041
Spinal-Multiple-Myeloma-SEG, vertebrae and lytic lesionsTotalSegmentator (total), the authors' package2Dice0.8221
LIDC-annot-NLST501TotalSegmentator (lung_nodules), the authors' package1Dice0.288040
NLSTsegTotalSegmentator (lung_nodules), the authors' package1Dice0.557041
PDDCA, head and neck organs at riskTotalSegmentator (craniofacial_structures), the authors' package1Dice0.654038
PDDCA, head and neck organs at riskTotalSegmentator (head_glands_cavities), the authors' package2Dice0.566026
PENGWIN CTTotalSegmentator (total), the authors' package1Dice0.9260
PENGWIN CTTotalSegmentator (total), KonfAI app2Dice0.925020
PENGWIN CTMRSegmentator, KonfAI app4Dice0.6323
PROMISE12, prostateTotalSegmentator (total_mr), the authors' package1Dice0.774018
PROMISE12, prostateTotalSegmentator (total_mr), KonfAI app2Dice0.720014
Pancreas-CT, 8 organsTotalSegmentator (total), KonfAI app1Dice0.841021
Pancreas-CT, 8 organsTotalSegmentator (total), the authors' package2Dice0.8400
Pancreas-CT, 8 organsMRSegmentator, KonfAI app5Dice0.156477
Pancreatic-CT-CBCT-SEG, bowel on the planning CTMRSegmentator, KonfAI app1Dice0.072054
Pancreatic-CT-CBCT-SEG, bowel on the planning CTTotalSegmentator (total), the authors' package2Dice0.0740
Pancreatic-CT-CBCT-SEG, bowel on the planning CTTotalSegmentator (total), KonfAI app3Dice0.0730
Pediatric-CT-SEG, organs of childrenTotalSegmentator (total), the authors' package2Dice0.6330
Pediatric-CT-SEG, organs of childrenTotalSegmentator (total), KonfAI app4Dice0.624017
Pediatric-CT-SEG, organs of childrenIMPACTSeg body, KonfAI app5Dice0.547215
Pediatric-CT-SEG, organs of childrenMRSegmentator, KonfAI app6Dice0.315831
Pediatric thoracic dynamic MRI, six organsTotalSegmentator (total_mr), the authors' package1Dice0.750023
Pediatric thoracic dynamic MRI, six organsTotalSegmentator (total_mr), KonfAI app2Dice0.737027
Pediatric thoracic dynamic MRI, six organsMRSegmentator, KonfAI app3Dice0.0670
PleThoraTotalSegmentator (pleural_pericard_effusion), the authors' package1Dice0.374045
Prostate-Anatomical-Edge-CasesTotalSegmentator (total), KonfAI app2Dice0.840035
Prostate-Anatomical-Edge-CasesTotalSegmentator (total), the authors' package3Dice0.8390
Prostate-MRI-US-Biopsy, the gland on MRTotalSegmentator (total_mr), the authors' package1Dice0.813019
Prostate-MRI-US-Biopsy, the gland on MRTotalSegmentator (total_mr), KonfAI app2Dice0.803021
Simulated thoracic CBCT, four clinical contoursIMPACTSeg body, KonfAI app1Dice0.80903
RCC-AIDMRSegmentator, KonfAI app1Dice0.8510
RCC-AIDTotalSegmentator (total), KonfAI app3Dice0.5990
RCC-AIDTotalSegmentator (total), the authors' package4Dice0.5540
RCC-AIDTotalSegmentator (kidney_cysts), the authors' package5Dice0.005024
RibSeg v2, individual ribsTotalSegmentator (total), the authors' package1Dice0.8050
RibSeg v2, individual ribsTotalSegmentator (total), KonfAI app2Dice0.7900
SAROS body regionsIMPACTSeg body, KonfAI app1Dice0.896025
SAROS body regionsTotalSegmentator (total), the authors' package2Dice0.820096
SAROS body regionsTotalSegmentator (total), KonfAI app3Dice0.815036
SAROS body regionsTotalSegmentator (head_glands_cavities), the authors' package4Dice0.640041
SAROS body regionsMRSegmentator, KonfAI app6Dice0.271033
Spine-generic, spinal cordTotalSegmentator (total_mr), the authors' package1Dice0.5130
Spine-generic, spinal cordTotalSegmentator (total_mr), KonfAI app2Dice0.4821
Spine-generic, spinal cordIMPACTSeg body, KonfAI app3Dice0.00008
Spine-Mets-CT-SEGTotalSegmentator (total), the authors' package1Dice0.8580
Spine-Mets-CT-SEGTotalSegmentator (total), KonfAI app2Dice0.8440
TotalSegmentator CTTotalSegmentator (total), the authors' package1Dice0.928085
TotalSegmentator CTTotalSegmentator (total), KonfAI app2Dice0.867029
TotalSegmentator CTIMPACTSeg body, KonfAI app3Dice0.789025
TotalSegmentator CTTotalSegmentator (kidney_cysts), the authors' package5Dice0.058027
TotalSegmentator MRI, any regionTotalSegmentator (total_mr), the authors' package1Dice0.718031
TotalSegmentator MRI, any regionTotalSegmentator (total_mr), KonfAI app2Dice0.631025
TotalSegmentator MRI, any regionIMPACTSeg body, KonfAI app3Dice0.105022
TotalSegmentator MRI, any regionMRSegmentator, KonfAI app4Dice0.039123
TotalSegmentator MRI, 50 structuresMRSegmentator, KonfAI app1Dice0.1830
TotalSegmentator MRI, 50 structuresIMPACTSeg body, KonfAI app2Dice0.0110
VerSe, vertebraeTotalSegmentator (total), KonfAI app1Dice0.574434
WAW-TACETotalSegmentator (liver_vessels), the authors' package1Dice0.572032
Source
huggingface.co/fideus-labs/fidopt-segmentation