[SEG] New segmentation tool candidates
Open, NormalPublic
Actions

Assigned To

None

Authored By

	floca
	Jun 1 2022, 5:03 PM

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.

Related Objects
Search...

Status	Assigned	Task
Open	None	T29191 [SEG] New segmentation tool candidates
Resolved	floca	T28464 [Segmentation] New Add/Remove tool
Resolved	kahl	T28406 [Segmentation] Examine Live-wire tool for different costfunctions/behavior
Resolved	j762e	T28851 [SEG] Add ITK GrowCut as segmentation tool
Open	None	T29192 [SEG] MONAI Label support in MITK Workbench
Open	a178n	T29295 MONAI Label App as auto-segmentation tool in MITK
Resolved	floca	T29451 [SEG] Response labels all not displayed on Workbench
Resolved	floca	T29500 [SEG] SegWithPreview tools with multiple labels are broken (if the produce a 0 label)
Open	None	T29452 Setting arbitrary label names to a LabelSetImage can be more straightforward
Open	None	T29455 Avoid image R/W to disk for MonaiLabel REST transactions
Open	a178n	T29379 MONAI Label REST Response JSON issues, allegedly
Open	None	T30147 MONAI Label: New approach using python wrapper??
Open	None	T30154 MONAI Label server usage issues
Open	None	T30151 MONAI Label tool support CLICK interaction patterns
Open	None	T29456 Datastore access facility in MONAILabel tool
Open	None	T30229 MONAI Label tool: Introduce time out parameter entry in Preferences
Open	a178n	T30231 Monailabel User documentation
Open	None	T30232 MONAI Label: Level Window contrast effects
Open	None	T30240 MonaiLabel: How to support more apps
Open	None	T30242 [MONAILabel] Trouble activating SSL support in Httplib
Open	a178n	T30247 MONAILabel: Improve doxygen docstrings
Spite	floca	T29193 [SEG] Add a superpixel tool
Open	None	T28499 Refactor/rewrite RegionGrowing3D tool
Open	None	T28275 [Segmentation] AdaptiveRegionGrowingTool must be refactored / 4D Segmentation returns error message when point is not on the correct timestep
Wontfix	None	T27872 [Segmentation] Region Growing 3D GUI does not provide a "Overwrite" checkbox
Open	None	T27684 [Segmentation] Improve Region Growing 2D algorithm and interaction
Resolved	kislinsk	T27437 Migrate MITK to use ITK 5.x
Wontfix	None	T26413 Nifti2 support
Duplicate	None	T26456 Update ITK to v5
Resolved	floca	T28446 Migrate MatchPoint to ITK v5.1
Resolved	a178n	T28523 Evaluate MITK segmentation survey
Open	None	T29309 [GrowCut] Further remarks regarding GrowCut
Resolved	kislinsk	T29310 [ITK] Check if ITK 5.3 adds the GrowCut remote module by default
Resolved	floca	T29311 Further observation of the GrowCut segmentation tool on 4D images
Resolved	s434n	T29312 Add support for using layers other than layer 0 of the current LabelSetImage
Open	None	T29313 Add a Test to check if the GrowCut algorithm produces a different output
Open	None	T29562 [GrowCut] "Undo" only changes slices with seed images
Open	None	T29437 [SEG] Add TotalSegmentator
Resolved	a178n	T29457 Introduce basic TotalSegmentator tool in Workbench
Resolved	a178n	T29458 Include Advanced settings support for TotalSegmentator tool in MITK
Open	None	T29465 How to display available statistics of segmentation
Open	None	T29459 Docker support for TotalSegmentator
Resolved	None	T29461 TotalSegmentator output label names conundrum
Resolved	a178n	T29462 TotalSegmentator (Python) issues
Resolved	a178n	T29463 Doxygen documentation for TotalSegmentator
Resolved	a178n	T29464 Test plan for TotalSegmentator
Resolved	a178n	T29468 Let MITK handle TotalSegmentator setup
Open	None	T29485 TotalSegmentator User Testing
Open	None	T29487 Tool Icon for TotalSegmentator
Resolved	a178n	T29497 Full support for all subtasks
Open	None	T29510 Migrate installer from Qt GUI level to MITK level
Resolved	a178n	T29538 Test with latest Totalsegmentator v1.5.5
Resolved	a178n	T29558 TotalSegmentator: Modify as per new Segmentation changes
Resolved	a178n	T29560 TotalSegmentator Label naming scheme
Resolved	a178n	T29566 TotalSegmentator GUI bug: Install button not Activated correctly
Resolved	a178n	T29567 TotalSeg: inferencing issue on MacOS
Resolved	a178n	T29569 [Checklist] Update TotalSegmentator & nnUNet checklist
Open	None	T29596 Move out FAST checkbox from Advanced
Open	a178n	T29597 TotalSeg didn't remember python environment
Resolved	a178n	T30215 [SEG] Support TotalSegmentatorV2
Resolved	None	T30256 TotalSeg: Add check for Python version
Resolved	a178n	T30300 Remember "Fast" checkbox setting
Open	None	T30301 Move Totalsegmentator installation into Preferences
Open	a178n	T30353 [TotalSeg] Add confirmation dialog before exiting the tool
Open	None	T29524 SAM in MITK
Resolved	a178n	T29539 SAM Python wrapper for MITK
Open	None	T29648 SAM Python: Improve the wrapper to be used independently without MITK
Resolved	a178n	T29540 SAM as 2D tool in MITK
Resolved	a178n	T29604 SAM as 2D Tool in MITK- iteration 2
Resolved	a178n	T29635 SAM tool: Cannot Confirm segmentation properly
Resolved	a178n	T29644 Doxygen documentation for SAM
Resolved	a178n	T29645 Test Plan for SAM
Open	a178n	T29651 [Preferences] SAM tool Preferences not rendered nicely on MacOS
Open	None	T29652 [Preferences] Cannot open SAM preference page after tool activation
Open	None	T29653 SAM tool: Install process can be non-blocking
Open	None	T29654 SAM tool: Preview not fully cleared when Reset Picks button is clicked
Resolved	a178n	T29655 SAM tool: Enable 2D RGB image support
Resolved	a178n	T30146 SAMtool: Problem while downloading pretrained models
Resolved	a178n	T30153 SAM tool: Add caching support for Cross-hair rotated image views
Resolved	a178n	T30156 Level Window contrast effect in SAM tool
Resolved	a178n	T30220 SAM tool: Custom NRRD writer not working as expected in Ubuntu
Resolved	a178n	T30253 SAM tool: Installation could show error message for wrong python path
Resolved	a178n	T30263 [Segmentation] SAM tool issue with single slice (2D)
Open	None	T30313 SegmentAnyBone in MITK
Open	None	T30314 MedSAM in MITK
Open	a178n	T30354 [MedSAM] Update SAM python daemon script for MedSAM
Open	a178n	T30355 [Seg] MedSAM as new 2D Tool in MITK
Open	a178n	T30356 [MedSAM] Create Test user checklist
Open	a178n	T30357 [MedSAM] Add user documentaiton