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Nov 29 2022

a178n edited projects for T29295: MONAI Label App as auto-segmentation tool in MITK, added: MITK (v2023.04); removed MITK, Next Milestone.
Nov 29 2022, 10:22 AM · MITK (v2024.06)

Nov 28 2022

floca added a comment to T27189: REST API for data storage.

OK. Thanks for the clarification.

Nov 28 2022, 9:31 AM · MITK (v2024.06), Restricted Project, Request for Discussion

Nov 25 2022

kislinsk moved T29025: Preference service (access) based on cpp microservices from Backlog to Cycle on the MITK (v2023.04) board.
Nov 25 2022, 10:45 PM · MITK (v2023.04), Breaking Change
kislinsk edited projects for T29025: Preference service (access) based on cpp microservices, added: Breaking Change, MITK (v2023.04); removed Request for Discussion, MITK.

Migration guide and a ton of examples can be found in {D763}.

Nov 25 2022, 10:45 PM · MITK (v2023.04), Breaking Change
kislinsk added a revision to T29025: Preference service (access) based on cpp microservices: Unknown Object (Differential Revision).
Nov 25 2022, 10:44 PM · MITK (v2023.04), Breaking Change
floca added a comment to T27718: Miniapp for basic DICOM testing.

Discussion result: nice to have wären auch die Informationen des "first pass" (-> welche reader configuratoin, findet wieviele volumes und welche Dateien werden verwendet) schön.

Nov 25 2022, 2:11 PM · MITK (v2023.12), Kaapana (internal)
gaoh added a comment to T27189: REST API for data storage.

So the last changes in the branch, are basically the changes I made, so that she could modify the code, already used for the dicomweb/kaapana interaction, to simply apply it for this modul. Since it would have been quite similar. I guess, when the changes of the rest module are done: We (AIH-Cluster will take care of restarting the MITK-Kaapana interaction). I think this could be then a not so complicated add-on.

Nov 25 2022, 12:16 PM · MITK (v2024.06), Restricted Project, Request for Discussion
gaoh added a comment to T27189: REST API for data storage.

Oh yes, I also forgot about this, the final state was, as I remember correctly, that she did not succeed in producing meaningful results.

Nov 25 2022, 12:12 PM · MITK (v2024.06), Restricted Project, Request for Discussion
s434n moved T29284: Refactor segmentation plugin user manual documentation from Backlog to Segmentation on the MITK (v2023.04) board.
Nov 25 2022, 12:04 PM · MITK (v2024.06)
s434n merged task T16153: [Segmentation] Jump to center of mass of segmentation on click into T29354: Double-clicking a label jumps to the label but not its centroid.
Nov 25 2022, 11:57 AM · MITK (v2023.04), Bugzilla
s434n merged T16153: [Segmentation] Jump to center of mass of segmentation on click into T29354: Double-clicking a label jumps to the label but not its centroid.
Nov 25 2022, 11:57 AM · MITK (v2023.04)
floca added a parent task for T25192: Enable DICOM SEG conversion for nrrd segmentations: T27178: MITK - DICOM Seg - loaded DCM SEG not associated with referenced DCM .
Nov 25 2022, 11:36 AM · MITK (v2024.06), MICO (Demo MICCAI 2018)
floca added a subtask for T27178: MITK - DICOM Seg - loaded DCM SEG not associated with referenced DCM : T25192: Enable DICOM SEG conversion for nrrd segmentations.
Nov 25 2022, 11:36 AM · Auto-closed, Missing Info, MITK
floca reopened T27178: MITK - DICOM Seg - loaded DCM SEG not associated with referenced DCM as "Open".
Nov 25 2022, 11:31 AM · Auto-closed, Missing Info, MITK
floca moved T27189: REST API for data storage from Backlog to In candidates on the MITK (v2023.04) board.
Nov 25 2022, 11:28 AM · MITK (v2024.06), Restricted Project, Request for Discussion
floca edited projects for T27189: REST API for data storage, added: MITK (v2023.04); removed MITK, Next Milestone.
Nov 25 2022, 11:27 AM · MITK (v2024.06), Restricted Project, Request for Discussion
floca added a comment to T27189: REST API for data storage.

@gaoh Please help me out. what was the final status of Elisabth's work here? Totaly dropped off the radar.

Nov 25 2022, 11:27 AM · MITK (v2024.06), Restricted Project, Request for Discussion
floca added a parent task for T29389: Python utility module: T29390: How to ease the handling of external generated segmentations.
Nov 25 2022, 11:17 AM · MITK (v2024.06)
floca added a subtask for T29390: How to ease the handling of external generated segmentations: T29389: Python utility module.
Nov 25 2022, 11:17 AM · MITK (v2024.06)
floca moved T29390: How to ease the handling of external generated segmentations from Backlog to In candidates on the MITK (v2023.04) board.
Nov 25 2022, 11:15 AM · MITK (v2024.06)
floca edited projects for T29390: How to ease the handling of external generated segmentations, added: MITK (v2023.04); removed MITK.
Nov 25 2022, 11:14 AM · MITK (v2024.06)
floca added a comment to T29390: How to ease the handling of external generated segmentations.

this is also partially covered/related with T29392: [SEG] Add dedicated writer to store multi-label images in nifti

Nov 25 2022, 11:14 AM · MITK (v2024.06)
floca moved T27718: Miniapp for basic DICOM testing from Backlog to In candidates on the MITK (v2023.04) board.
Nov 25 2022, 11:08 AM · MITK (v2023.12), Kaapana (internal)
floca edited projects for T27718: Miniapp for basic DICOM testing, added: MITK (v2023.04); removed MITK.
Nov 25 2022, 11:07 AM · MITK (v2023.12), Kaapana (internal)

Nov 24 2022

kislinsk added a comment to T29025: Preference service (access) based on cpp microservices.

Pushed new branch to rMITK MITK: feature/T29025-PreferencesCoreService.

Nov 24 2022, 4:55 PM · MITK (v2023.04), Breaking Change
floca closed T28135: [MultiLabel Segmentation] Utilities view cannot handle non-binary multilabel segmentations as Resolved.
Nov 24 2022, 2:37 PM · MITK (v2023.04)
floca closed T28135: [MultiLabel Segmentation] Utilities view cannot handle non-binary multilabel segmentations, a subtask of T28936: [Segmentation] Remove utilities redundancy with MultiLabelSegmentation, as Resolved.
Nov 24 2022, 2:37 PM · MITK (v2022.10), Breaking Change
floca moved T28139: [LabelSetImage] Ambigious meaning of "layer" in LabelSetImage from Backlog to Segmentation on the MITK (v2023.04) board.
Nov 24 2022, 2:36 PM · MITK (v2023.12), Request for Discussion
floca moved T28140: [MultiLabel Segmentation] Default parameter (unsigned int layer = 0) is unnecessary and causes problems from Backlog to Segmentation on the MITK (v2023.04) board.
Nov 24 2022, 2:36 PM · MITK (v2024.06)
floca moved T28262: TimeGeometry inconsistent documentation and implementation of time bounds and checks from Backlog to Others on the MITK (v2023.04) board.
Nov 24 2022, 2:28 PM · MITK (v2024.06)
floca moved T28479: [Segmentation] Rethink / reevaluate our existing segmentation tools / algorithms from Backlog to Segmentation on the MITK (v2023.04) board.
Nov 24 2022, 2:27 PM · MITK (v2024.06)
floca moved T28675: Boolean Operations in Segmentation utilities are slow from Backlog to Segmentation on the MITK (v2023.04) board.
Nov 24 2022, 2:24 PM · MITK (v2024.06), Request for Discussion
floca moved T28752: [Segmentation] Move Segmentation utilities widgets to SegmentationUI module from Backlog to Segmentation on the MITK (v2023.04) board.
Nov 24 2022, 2:24 PM · MITK (v2023.04)
floca moved T28797: [Segmentation[MultiLabel][Utilities] Using 4D data with dynamic segmentations results in 3D data from Backlog to Segmentation on the MITK (v2023.04) board.
Nov 24 2022, 2:09 PM · MITK (v2024.06), Checklist
floca moved T29098: [3D Segmentation] UL Threshold Tool - 0 intensity value not include in slider range? from Backlog to Segmentation on the MITK (v2023.04) board.
Nov 24 2022, 2:03 PM · MITK (v2024.06), Restricted Project, Checklist
floca moved T28785: Levelwindow UX proposals/comments from Backlog to Segmentation on the MITK (v2023.04) board.
Nov 24 2022, 2:03 PM · MITK (v2024.06), Checklist, Missing Info, Request for Discussion
floca moved T28791: [Segmentation][Multilabel][Options]"Create polygon model" issues for large images from Backlog to Segmentation on the MITK (v2023.04) board.
Nov 24 2022, 2:01 PM · MITK (v2024.06), Checklist
floca moved T28796: [Segmentation][Utilities] Morphological Operations behave unexpectedly from Backlog to Segmentation on the MITK (v2023.04) board.
Nov 24 2022, 2:01 PM · MITK (v2024.06), Checklist
floca moved T29157: NCT ISSO Annotation Support with MITK Segmentation Flow from Backlog to Segmentation on the MITK (v2023.04) board.
Nov 24 2022, 1:56 PM · MITK (v2024.06)
floca moved T29168: [Multilabel Segmentation] Definition and usage of masking and maskstamping from Backlog to Segmentation on the MITK (v2023.04) board.
Nov 24 2022, 1:56 PM · MITK (v2024.06)
floca moved T29191: [SEG] New segmentation tool candidates from Backlog to Segmentation on the MITK (v2023.04) board.
Nov 24 2022, 12:22 PM · MITK (v2024.06)
floca moved T29192: [SEG] MONAI Label support in MITK Workbench from Backlog to Segmentation on the MITK (v2023.04) board.
Nov 24 2022, 12:21 PM · MITK (v2024.06)
floca added a comment to T29193: [SEG] Add a superpixel tool.

One thing to consider might be, is SLIC even useful? If neural networks are going to be taking care of segmentation anyway, what is it's likely sell-by date? This depends on how quickly NN based segmentation algorithms are incorporated into MITK.

Nov 24 2022, 12:21 PM · MITK (v2024.06)
floca moved T29193: [SEG] Add a superpixel tool from Backlog to Segmentation on the MITK (v2023.04) board.
Nov 24 2022, 12:15 PM · MITK (v2024.06)
floca moved T29197: [Segmentation] Is the classificationsegmentation-plugin used / required? from Backlog to Segmentation on the MITK (v2023.04) board.
Nov 24 2022, 12:12 PM · MITK (v2024.06)
floca added a project to T29197: [Segmentation] Is the classificationsegmentation-plugin used / required?: Request for Discussion.
Nov 24 2022, 12:12 PM · MITK (v2024.06)
floca moved T29204: [SEG] Rework properties of Label class + add instance information from Backlog to Segmentation on the MITK (v2023.04) board.
Nov 24 2022, 12:11 PM · MITK (v2024.06), Breaking Change
floca moved T29285: [Checklist] Revise Remeshing checklist from Backlog to Tests/Checklists on the MITK (v2023.04) board.
Nov 24 2022, 12:11 PM · MITK (v2023.04), Checklist
floca moved T29310: [ITK] Check if ITK 5.3 adds the GrowCut remote module by default from Backlog to Segmentation on the MITK (v2023.04) board.
Nov 24 2022, 12:10 PM · MITK (v2023.12)
floca closed T29311: Further observation of the GrowCut segmentation tool on 4D images, a subtask of T29309: [GrowCut] Further remarks regarding GrowCut, as Resolved.
Nov 24 2022, 12:10 PM · MITK
floca closed T29311: Further observation of the GrowCut segmentation tool on 4D images as Resolved.
Nov 24 2022, 12:10 PM · MITK (v2023.04)
floca moved T29337: Global Reinit HotKey functionality not there in Mac OSX from Backlog to Others on the MITK (v2023.04) board.
Nov 24 2022, 12:09 PM · MITK (v2024.06), Cleared, Checklist
floca closed T29346: Level Window Checklist - Level Window slider inconsistent upper/lower bound behavior on mouse clicks. as Resolved.
Nov 24 2022, 12:07 PM · MITK (v2023.04), Cleared
neher triaged T29417: Segmentation view crashes on loading binary image as Normal priority.
Nov 24 2022, 12:01 PM · MITK
neher added a comment to T29416: Segmentation utilities can only handle unsigned char and unsigned short, no other types.

Example data

Nov 24 2022, 11:57 AM · MITK (v2024.06), Missing Info
kalali removed a subtask for T29210: Clarify / remove axis-labeling for anatomical planes: T29211: Remove "Scaling" from QmitkRegistrationManipulationWidget.ui.
Nov 24 2022, 10:44 AM · MITK (v2024.06), Request for Discussion
kalali removed a parent task for T29211: Remove "Scaling" from QmitkRegistrationManipulationWidget.ui: T29210: Clarify / remove axis-labeling for anatomical planes.
Nov 24 2022, 10:44 AM · MITK
kalali removed a subtask for T26543: Enum for AXIAL, SAGITTAL, CORONAL 3D/ORIGINAL/NONE is provided at many different locations: T29210: Clarify / remove axis-labeling for anatomical planes.
Nov 24 2022, 10:44 AM · Breaking Change, Noteworthy, MITK
kalali removed a parent task for T29210: Clarify / remove axis-labeling for anatomical planes: T26543: Enum for AXIAL, SAGITTAL, CORONAL 3D/ORIGINAL/NONE is provided at many different locations.
Nov 24 2022, 10:44 AM · MITK (v2024.06), Request for Discussion
kalali closed T26543: Enum for AXIAL, SAGITTAL, CORONAL 3D/ORIGINAL/NONE is provided at many different locations as Resolved.
Nov 24 2022, 10:43 AM · Breaking Change, Noteworthy, MITK
floca moved T28264: [Segmentation Utilities] Various issues from Backlog to Segmentation on the MITK (v2023.04) board.
Nov 24 2022, 10:39 AM · MITK (v2024.06), Cleared
floca moved T28561: Refactor/Fix mitk::SegmentationInteractor::ChangeActiveLabel from Backlog to Segmentation on the MITK (v2023.04) board.
Nov 24 2022, 10:39 AM · MITK (v2024.06)
kalali committed rMITK748b94b4186d: Merge enums for view direction (authored by kalali).
Merge enums for view direction
Nov 24 2022, 10:38 AM
kalali committed rMITK513e872beb07: Replace ViewDirection with AnatomicalPlane (authored by kalali).
Replace ViewDirection with AnatomicalPlane
Nov 24 2022, 10:38 AM
kalali committed rMITKc0f6326f8503: Use anatomical plane in depending classes (authored by kalali).
Use anatomical plane in depending classes
Nov 24 2022, 10:38 AM
kalali committed rMITK4d4c91e4f9b5: Replace ViewDirection and PlaneOrientation with AnatomicalPlane (authored by kalali).
Replace ViewDirection and PlaneOrientation with AnatomicalPlane
Nov 24 2022, 10:38 AM

Nov 23 2022

floca moved T28500: Multilabel Segmentation Utilities do not work for multilabel segmentations from Backlog to Segmentation on the MITK (v2023.04) board.
Nov 23 2022, 6:16 PM · MITK (v2024.06), Missing Info
floca moved T28798: [Segmentation][MultiLabel][Utilities] UI is inconsistent / unstable from Backlog to Segmentation on the MITK (v2023.04) board.
Nov 23 2022, 6:16 PM · MITK (v2024.06), Checklist
floca moved T29105: [3D Surface Interpolation] 3D+t Interpolation Preview Crashes When Going Through Different Time Steps from Backlog to Cycle on the MITK (v2023.04) board.
Nov 23 2022, 5:48 PM · Breaking Change, MITK (v2024.06), Checklist
floca moved T29225: Rule Checker for FlowBench from Backlog to Cycle on the MITK (v2023.04) board.
Nov 23 2022, 5:48 PM · MITK
floca moved T29396: [Segmentation] Newly created labelset image has wrong image type from Backlog to In candidates on the MITK (v2023.04) board.
Nov 23 2022, 5:46 PM · MITK (v2024.06)
floca edited projects for T29396: [Segmentation] Newly created labelset image has wrong image type, added: MITK (v2023.04); removed MITK.
Nov 23 2022, 5:46 PM · MITK (v2024.06)
floca moved T29416: Segmentation utilities can only handle unsigned char and unsigned short, no other types from Backlog to In candidates on the MITK (v2023.04) board.
Nov 23 2022, 5:46 PM · MITK (v2024.06), Missing Info
kalali updated the task description for T26543: Enum for AXIAL, SAGITTAL, CORONAL 3D/ORIGINAL/NONE is provided at many different locations.
Nov 23 2022, 5:45 PM · Breaking Change, Noteworthy, MITK
floca edited projects for T29416: Segmentation utilities can only handle unsigned char and unsigned short, no other types, added: MITK (v2023.04), Missing Info; removed MITK.

Which data has been used to provoke the problem.

Nov 23 2022, 5:44 PM · MITK (v2024.06), Missing Info
kalali committed rMITK6cd2ce96452e: Show pixel value for mxnmultiwidget (authored by kalali).
Show pixel value for mxnmultiwidget
Nov 23 2022, 5:40 PM
kalali committed rMITK674aee77ff2a: React on render window part changed (authored by kalali).
React on render window part changed
Nov 23 2022, 5:40 PM
kalali committed rMITK0d6a33f237fd: Clean up some classes (authored by kalali).
Clean up some classes
Nov 23 2022, 5:40 PM
kalali committed rMITK0a152488cdfb: React on the GeometryUpdateEvent of the SliceNavigationController (authored by kalali).
React on the GeometryUpdateEvent of the SliceNavigationController
Nov 23 2022, 5:40 PM
kalali committed rMITKddec35e41d7d: Update the crosshair with a new slice (authored by kalali).
Update the crosshair with a new slice
Nov 23 2022, 5:40 PM
kalali claimed T29385: [mxn multi widget] Pixel value view does not change on crosshair selection.
Nov 23 2022, 5:03 PM · MITK (v2023.04)
kalali closed T29388: [Segmentation] Loading a nifti segmentation (nii) leads to a crash as Resolved.
Nov 23 2022, 4:55 PM · MITK
kalali removed a parent task for T29392: [SEG] Add dedicated writer to store multi-label images in nifti: T29388: [Segmentation] Loading a nifti segmentation (nii) leads to a crash.
Nov 23 2022, 4:54 PM · MITK (v2024.06)
kalali removed a subtask for T29388: [Segmentation] Loading a nifti segmentation (nii) leads to a crash: T29392: [SEG] Add dedicated writer to store multi-label images in nifti.
Nov 23 2022, 4:54 PM · MITK
kalali committed rMITK108795e0fc1f: Disable selecting legacy binary segmentations (authored by kalali).
Disable selecting legacy binary segmentations
Nov 23 2022, 4:52 PM
kalali committed rMITK00c6c35f7a3d: Remove binary segmentations as valid selection input (authored by kalali).
Remove binary segmentations as valid selection input
Nov 23 2022, 4:52 PM
kalali committed rMITK0601cbfc6a6a: Fix crash when loading multilabel nifty segmentations (authored by kalali).
Fix crash when loading multilabel nifty segmentations
Nov 23 2022, 4:51 PM
kalali committed rMITK48d2214579c5: Add nullptr checks for legacy, binary segmentations (authored by kalali).
Add nullptr checks for legacy, binary segmentations
Nov 23 2022, 4:51 PM
floca moved T27319: [Segmentation] Correctly implement interpolation features for Multilabel Segmentation View from Backlog to Cycle on the MITK (v2023.04) board.
Nov 23 2022, 3:55 PM · MITK (v2023.04), Restricted Project
floca moved T26172: 2D interpolation in MultiLabelSegmentation Editor only works for 1. label from Backlog to Cycle on the MITK (v2023.04) board.
Nov 23 2022, 3:55 PM · MITK (v2023.04)
floca moved T28275: [Segmentation] AdaptiveRegionGrowingTool must be refactored / 4D Segmentation returns error message when point is not on the correct timestep from Backlog to Cycle on the MITK (v2023.04) board.
Nov 23 2022, 3:55 PM · MITK (v2024.06)
floca moved T28491: [Segmentation] Slice interpolation 'confirm for all slices' sometimes crahes from Backlog to Cycle on the MITK (v2023.04) board.
Nov 23 2022, 3:55 PM · MITK (v2023.12)
floca moved T28499: Refactor/rewrite RegionGrowing3D tool from Backlog to Cycle on the MITK (v2023.04) board.
Nov 23 2022, 3:55 PM · MITK (v2024.06)
floca moved T29060: [Segmentation] Glitch in label color after 3d-interpolation from Backlog to Cycle on the MITK (v2023.04) board.
Nov 23 2022, 3:55 PM · MITK (v2023.04), Checklist
floca moved T29063: When all the folds are selected in "Folds" dropdown box, then show "All Folds" instead of "All" from Backlog to Cycle on the MITK (v2023.04) board.
Nov 23 2022, 3:55 PM · MITK (v2024.06)
floca moved T29067: Introduce option to save the segmentation in the nnUNet tool GUI itself. from Backlog to Cycle on the MITK (v2023.04) board.
Nov 23 2022, 3:55 PM · MITK
floca moved T29077: [Segmentation] Showing / hiding labels using the labelsetwidget selects them from Backlog to Cycle on the MITK (v2023.04) board.
Nov 23 2022, 3:55 PM · MITK (v2023.04), Checklist
floca moved T29206: [SEG] Implement a Qt model for LabelSets for MVC patterns from Backlog to Cycle on the MITK (v2023.04) board.
Nov 23 2022, 3:55 PM · MITK (v2023.04), Checklist
floca moved T29347: Measurement Checklist - Possible inconsistent recentering behavior when clicking on geometry node in Data Manager. from Backlog to Cycle on the MITK (v2023.04) board.
Nov 23 2022, 3:55 PM · Request for Discussion, Checklist
floca moved T29352: Segmentation Options Checklist - "Create Smoothed Polygon" Seems Not to Work from Backlog to Cycle on the MITK (v2023.04) board.
Nov 23 2022, 3:55 PM · MITK (v2024.06), Cleared, Checklist