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Maniphest T29191

[SEG] New segmentation tool candidates
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Description

this is a meta task to collect any new potential additions to the segmentation tools.

Subtasks of this task are a collection of possibilities. It is not implied that all will have to be implemented. We will assess (technical proof of concept, uses survey) them later on to see if an addition is worth it.

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StatusAssignedTask
 ResolvedkislinskT29191 [SEG] New segmentation tool candidates
 ResolvedflocaT28464 [Segmentation] New Add/Remove tool
 ResolvedkahlT28406 [Segmentation] Examine Live-wire tool for different costfunctions/behavior
 Resolvedj762eT28851 [SEG] Add ITK GrowCut as segmentation tool
 ResolvedkislinskT29192 [SEG] MONAI Label support in MITK Workbench
 Resolveda178nT29295 MONAI Label App as auto-segmentation tool in MITK
 ResolvedflocaT29451 [SEG] Response labels all not displayed on Workbench
 ResolvedflocaT29500 [SEG] SegWithPreview tools with multiple labels are broken (if the produce a 0 label)
 ResolvedkislinskT29452 Setting arbitrary label names to a LabelSetImage can be more straightforward
 ResolvedkislinskT29455 Avoid image R/W to disk for MonaiLabel REST transactions
 Resolveda178nT29379 MONAI Label REST Response JSON issues, allegedly
 ResolvedkislinskT30147 MONAI Label: New approach using python wrapper??
 ResolvedkislinskT30154 MONAI Label server usage issues
 ResolvedkislinskT30151 MONAI Label tool support CLICK interaction patterns
 ResolvedkislinskT29456 Datastore access facility in MONAILabel tool
 ResolvedkislinskT30229 MONAI Label tool: Introduce time out parameter entry in Preferences
 Resolveda178nT30231 Monailabel User documentation
 ResolvedkislinskT30232 MONAI Label: Level Window contrast effects
ResolvedkislinskT30240 MonaiLabel: How to support more apps
 ResolvedkislinskT30242 [MONAILabel] Trouble activating SSL support in Httplib
 Resolveda178nT30247 MONAILabel: Improve doxygen docstrings
 SpiteflocaT29193 [SEG] Add a superpixel tool
 ResolvedkislinskT28499 Refactor/rewrite RegionGrowing3D tool
 ResolvedkislinskT28275 [Segmentation] AdaptiveRegionGrowingTool must be refactored / 4D Segmentation returns error message when point is not on the correct timestep
 WontfixNoneT27872 [Segmentation] Region Growing 3D GUI does not provide a "Overwrite" checkbox
 ResolvedkislinskT27684 [Segmentation] Improve Region Growing 2D algorithm and interaction
 ResolvedkislinskT27437 Migrate MITK to use ITK 5.x
WontfixNoneT26413 Nifti2 support
 DuplicateNoneT26456 Update ITK to v5
 ResolvedflocaT28446 Migrate MatchPoint to ITK v5.1
 Resolveda178nT28523 Evaluate MITK segmentation survey
 OpenNoneT29309 [GrowCut] Further remarks regarding GrowCut
 ResolvedkislinskT29310 [ITK] Check if ITK 5.3 adds the GrowCut remote module by default
 ResolvedflocaT29311 Further observation of the GrowCut segmentation tool on 4D images
 Resolveds434nT29312 Add support for using layers other than layer 0 of the current LabelSetImage
 OpenNoneT29313 Add a Test to check if the GrowCut algorithm produces a different output
 ResolvedkislinskT29562 [GrowCut] "Undo" only changes slices with seed images
 ResolvedflocaT29437 [SEG] Add TotalSegmentator
 Resolveda178nT29457 Introduce basic TotalSegmentator tool in Workbench
 Resolveda178nT29458 Include Advanced settings support for TotalSegmentator tool in MITK
 WontfixflocaT29465 How to display available statistics of segmentation
 ResolvedkislinskT29459 Docker support for TotalSegmentator
 ResolvedNoneT29461 TotalSegmentator output label names conundrum
 Resolveda178nT29462 TotalSegmentator (Python) issues
 Resolveda178nT29463 Doxygen documentation for TotalSegmentator
 Resolveda178nT29464 Test plan for TotalSegmentator
 Resolveda178nT29468 Let MITK handle TotalSegmentator setup
 ResolvedkislinskT29485 TotalSegmentator User Testing
ResolvedkislinskT29487 Tool Icon for TotalSegmentator
 Resolveda178nT29497 Full support for all subtasks
 ResolvedkislinskT29510 Migrate installer from Qt GUI level to MITK level
 Resolveda178nT29538 Test with latest Totalsegmentator v1.5.5
 Resolveda178nT29558 TotalSegmentator: Modify as per new Segmentation changes
 Resolveda178nT29560 TotalSegmentator Label naming scheme
 Resolveda178nT29566 TotalSegmentator GUI bug: Install button not Activated correctly
 Resolveda178nT29567 TotalSeg: inferencing issue on MacOS
 Resolveda178nT29569 [Checklist] Update TotalSegmentator & nnUNet checklist
 ResolvedkislinskT29596 Move out FAST checkbox from Advanced
 Resolveda178nT29597 TotalSeg didn't remember python environment
 Resolveda178nT30215 [SEG] Support TotalSegmentatorV2
 ResolvedNoneT30256 TotalSeg: Add check for Python version
 Resolveda178nT30300 Remember "Fast" checkbox setting
 ResolvedkislinskT30301 Move Totalsegmentator installation into Preferences
 Resolveda178nT30353 [TotalSeg] Add confirmation dialog before exiting the tool
Wontfixa178nT30447 [TotalSeg] Levelwindow effect
 Resolveda178nT30457 Add TotalSegmentator MR image (v 2.2) support in MITK
 ResolvedkislinskT29524 SAM in MITK
 Resolveda178nT29539 SAM Python wrapper for MITK
 ResolvedkislinskT29648 SAM Python: Improve the wrapper to be used independently without MITK
 Resolveda178nT29540 SAM as 2D tool in MITK
 Resolveda178nT29604 SAM as 2D Tool in MITK- iteration 2
 Resolveda178nT29635 SAM tool: Cannot Confirm segmentation properly
 Resolveda178nT29644 Doxygen documentation for SAM
 Resolveda178nT29645 Test Plan for SAM
 Resolveda178nT29651 [Preferences] SAM tool Preferences not rendered nicely on MacOS
 ResolvedkislinskT29652 [Preferences] Cannot open SAM preference page after tool activation
 ResolvedkislinskT29653 SAM tool: Install process can be non-blocking
 ResolvedkislinskT29654 SAM tool: Preview not fully cleared when Reset Picks button is clicked
 Resolveda178nT29655 SAM tool: Enable 2D RGB image support
 Resolveda178nT30146 SAMtool: Problem while downloading pretrained models
 Resolveda178nT30153 SAM tool: Add caching support for Cross-hair rotated image views
 Resolveda178nT30156 Level Window contrast effect in SAM tool
 Resolveda178nT30220 SAM tool: Custom NRRD writer not working as expected in Ubuntu
 Resolveda178nT30253 SAM tool: Installation could show error message for wrong python path
 Resolveda178nT30263 [Segmentation] SAM tool issue with single slice (2D)
 InvalidNoneT30398 3D interpolation using SAM tool
 Resolveda178nT30403 3D interpolation UX improvement using SAM tool
 Resolveda178nT30423 [SEG] Segment Anything misleading GPU message for first time users
 Resolveda178nT30426 [SEG] Highlight importance of level window in Segment Anything
 ResolvedkislinskT30427 [SEG] No status change message after changing model type to ‘vit_l’.
 ResolvedkislinskT30313 SegmentAnyBone in MITK
 ResolvedkislinskT30314 MedSAM in MITK
 Resolveda178nT30354 [MedSAM] Update SAM python daemon script for MedSAM
 Resolveda178nT30355 [Seg] MedSAM as new 2D Tool in MITK
 Resolveda178nT30356 [MedSAM] Create Test user checklist
 Resolveda178nT30357 [MedSAM] Add user documentaiton

Event Timeline

floca triaged this task as Normal priority.Jun 1 2022, 5:03 PM
floca created this task.
floca added subtasks: T28464: [Segmentation] New Add/Remove tool, T28406: [Segmentation] Examine Live-wire tool for different costfunctions/behavior, T28851: [SEG] Add ITK GrowCut as segmentation tool.Jun 1 2022, 5:06 PM
floca added a subtask: T29192: [SEG] MONAI Label support in MITK Workbench.Jun 1 2022, 5:12 PM
floca added a subtask: T29193: [SEG] Add a superpixel tool.Jun 1 2022, 5:20 PM
floca added subscribers: kalali, kislinsk.Jun 1 2022, 5:23 PM
kalali added a subscriber: j762e.Jun 7 2022, 2:00 PM
a178n added a subscriber: a178n.Jun 21 2022, 5:48 PM
floca moved this task from Backlog to Segmentation on the MITK (v2022.10) board.Jul 27 2022, 11:28 AM
floca closed subtask T28464: [Segmentation] New Add/Remove tool as Resolved.Aug 11 2022, 10:02 PM
kalali added a subtask: T28499: Refactor/rewrite RegionGrowing3D tool.Aug 15 2022, 9:37 AM
kislinsk closed subtask T28851: [SEG] Add ITK GrowCut as segmentation tool as Resolved.Oct 5 2022, 9:13 PM
kislinsk edited projects, added MITK (v2023.04); removed MITK (v2022.10).Nov 23 2022, 3:52 PM
floca moved this task from Backlog to Segmentation on the MITK (v2023.04) board.Nov 24 2022, 12:22 PM
kislinsk edited projects, added MITK (v2023.12); removed MITK (v2023.04).May 17 2023, 2:55 PM
kislinsk edited projects, added MITK (v2024.06); removed MITK (v2023.12).Dec 5 2023, 10:38 AM
floca closed subtask T28406: [Segmentation] Examine Live-wire tool for different costfunctions/behavior as Resolved.Feb 18 2024, 8:38 PM
floca closed subtask T29193: [SEG] Add a superpixel tool as Spite.Apr 19 2024, 9:04 AM
floca closed subtask T29437: [SEG] Add TotalSegmentator as Resolved.May 4 2024, 11:57 AM
kislinsk edited projects, added MITK (v2024.12); removed MITK (v2024.06).Jun 17 2024, 2:33 PM
kislinsk closed this task as Resolved.Sep 16 2024, 1:49 PM
kislinsk claimed this task.
kislinsk closed subtask T30314: MedSAM in MITK as Resolved.
kislinsk closed subtask T30313: SegmentAnyBone in MITK as Resolved.
kislinsk closed subtask T29524: SAM in MITK as Resolved.
kislinsk added a project: Moved to git.dkfz.de.

This task was closed here on Phabricator since it was migrated to GitLab. Please continue on GitLab.

kislinsk closed subtask T29192: [SEG] MONAI Label support in MITK Workbench as Resolved.Sep 16 2024, 1:49 PM
kislinsk closed subtask T28499: Refactor/rewrite RegionGrowing3D tool as Resolved.
MITK · MIC · IMSY · DKFZ