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kalali (Amir Kalali)
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Projects (6)

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User Since
Aug 1 2016, 12:10 PM (239 w, 6 d)

Recent Activity

Wed, Mar 3

kalali edited projects for T26485: PACS mode is active while segmentation is drawn, added: Request for Discussion, Next Milestone; removed Restricted Project.

Also when changing the interaction mode (PACS <-> MITK) while the segmentation tool (e.g. Add) is active, the changed interaction mode will overwrite the segmentation interaction and the render window changes again while drawing the segmentation.

Wed, Mar 3, 11:53 AM · Next Milestone, Request for Discussion, MITK

Tue, Mar 2

kalali committed rMITK7014777eedae: Preserve color selection (authored by kalali).
Preserve color selection
Tue, Mar 2, 9:11 AM
kalali committed rMITK372746b5a2ae: Initialize color member with red (authored by kalali).
Initialize color member with red
Tue, Mar 2, 9:11 AM
kalali committed rMITK93758e9b6fe4: Correctly initialize the color selection dialog (authored by kalali).
Correctly initialize the color selection dialog
Tue, Mar 2, 9:11 AM

Wed, Feb 24

kalali moved T27713: [Segmentation] Disable "New" button when no image is selected from Backlog to MITK Meeting on the Request for Discussion board.
Wed, Feb 24, 9:42 AM · Request for Discussion, MITK
kalali added a project to T27713: [Segmentation] Disable "New" button when no image is selected: Request for Discussion.
Wed, Feb 24, 9:42 AM · Request for Discussion, MITK
kalali moved T26959: Newly created LabelSet segmentation is not displayed as "outline binary" from Backlog to MITK Meeting on the Request for Discussion board.
Wed, Feb 24, 9:42 AM · MITK

Thu, Feb 18

kalali edited projects for T27713: [Segmentation] Disable "New" button when no image is selected, added: MITK; removed MITK (v2021.02).

I looked into it and I have the impression that there is a lot of unnecessary complexity created in order to generate a valid UI state. The problem, as far as I can see, lies in the overuse of if-conditions and having functions that have way to many responsibilities. This is a typical "clean code" task and I suggest to go through the whole QmitkSegmentationView.cpp file and apply some best practices of writing clean code.
But since it is not clear, how much effort we want to put into it (thinking of T28142), it might be wise to not work on this right now but to use a general refactoring task (parent task) to fix the mentioned bug.
I advise also to have a look https://phabricator.mitk.org/file/data/7bghshzurxwupnipv3dl/PHID-FILE-n2hwm6xv2mil3ola47sq/QtStateMachineFramework.pdf.

Thu, Feb 18, 4:18 PM · Request for Discussion, MITK

Tue, Feb 16

kalali edited projects for T26969: [Segmentation] New segmentation dialog: Change color twice and aborting the second time chages color to red, added: MITK; removed MITK (v2021.02).
Tue, Feb 16, 8:47 PM · MITK
kalali added a revision to T26969: [Segmentation] New segmentation dialog: Change color twice and aborting the second time chages color to red: Unknown Object (Differential Revision).
Tue, Feb 16, 7:18 PM · MITK
kalali claimed T26969: [Segmentation] New segmentation dialog: Change color twice and aborting the second time chages color to red.
Tue, Feb 16, 7:14 PM · MITK
kalali edited projects for T26959: Newly created LabelSet segmentation is not displayed as "outline binary", added: Request for Discussion, MITK; removed MITK (v2021.02).

It seems as if datanode->GetBoolProperty("binary", binary, renderer) inside mitkImageVtkMapper2D always results in binary being false. This might be true for our LabelSet images, but the properties view still shows the property binary as true, e.g. for segmentations created with the classic segmentation view.

Tue, Feb 16, 6:07 PM · MITK
kalali triaged T28315: [Selection concept] Provide preference page option to show / hide helper nodes as Normal priority.
Tue, Feb 16, 5:01 PM · MITK

Fri, Feb 12

kalali edited projects for T28138: [MultiLabel Segmentation] Add tests for the LabelSetImage, added: MITK; removed MITK (v2021.02).
Fri, Feb 12, 12:49 PM · MITK
kalali placed T28130: Extend "Checkliste MultiLabel Segmentierung – 3D Segmentierung" up for grabs.
Fri, Feb 12, 12:47 PM · MITK
kalali edited projects for T26956: LevelWindow slider does not expand the level/window scale, added: MITK; removed MITK (v2021.02).
Fri, Feb 12, 12:37 PM · MITK
kalali edited projects for T27907: Extend "Checkliste Documentation", added: MITK; removed MITK (v2021.02).
Fri, Feb 12, 12:36 PM · MITK, Cleared
kalali edited projects for T28265: [Checklist] Overhaul ViewNavigator checklists to be in line with the latest changes to the checklists, added: MITK; removed MITK (v2021.02).
Fri, Feb 12, 12:36 PM · MITK
kalali placed T27716: Extend "Checkliste Segmentierung – Manuelle Segmentierung / 2D Segmentierung" up for grabs.
Fri, Feb 12, 12:30 PM · MITK, Cleared
kalali lowered the priority of T27737: Extend "Checkliste Segmentierung – Optionen" from High to Normal.
Fri, Feb 12, 12:29 PM · MITK, Cleared
kalali placed T27850: Extend "Checkliste Segmentierung – 3D Segmentierung" up for grabs.
Fri, Feb 12, 12:29 PM · MITK, Cleared
kalali placed T27873: Extend "Checkliste Segmentierung – Manuelle Segmentierung mit Interpolation" up for grabs.
Fri, Feb 12, 12:28 PM · MITK, Cleared
kalali placed T27906: Extend "Checkliste Segmentierung – Utilities" up for grabs.
Fri, Feb 12, 12:28 PM · MITK, Cleared
kalali lowered the priority of T28110: Extend checklists for multilabel segmentation view from High to Normal.
Fri, Feb 12, 12:27 PM · MITK
kalali placed T28111: Extend "Checkliste MultiLabel Segmentierung – 2D Segmentierung" up for grabs.
Fri, Feb 12, 12:26 PM · MITK
kalali renamed T28108: [Release Checklists] Prepare release checklists from [Release Checklists] Prepare release checklists for Release 2021 to [Release Checklists] Prepare release checklists.
Fri, Feb 12, 12:25 PM · MITK
kalali lowered the priority of T28111: Extend "Checkliste MultiLabel Segmentierung – 2D Segmentierung" from High to Normal.
Fri, Feb 12, 12:24 PM · MITK
kalali lowered the priority of T28130: Extend "Checkliste MultiLabel Segmentierung – 3D Segmentierung" from High to Normal.
Fri, Feb 12, 12:24 PM · MITK
kalali lowered the priority of T28132: Extend "Checkliste MultiLabel Segmentierung – Interpolation" from High to Normal.
Fri, Feb 12, 12:23 PM · MITK
kalali lowered the priority of T28133: Extend "Checkliste MultiLabel Segmentierung – Utilities" from High to Normal.
Fri, Feb 12, 12:23 PM · MITK
kalali placed T28136: Extend "Checkliste MultiLabel Segmentierung – Optionen" up for grabs.
Fri, Feb 12, 12:22 PM · MITK
kalali placed T28191: Refactor and extend LevelWindow unit tests up for grabs.
Fri, Feb 12, 12:22 PM · MITK
kalali placed T26988: [Checklist] LevelWindow checklist does not provide explicit expected results for sufficient verification up for grabs.
Fri, Feb 12, 12:17 PM · MITK, Restricted Project
kalali lowered the priority of T28204: Refactor LevelWindowManagerTest from High to Normal.
Fri, Feb 12, 12:12 PM · MITK
kalali edited projects for T28204: Refactor LevelWindowManagerTest, added: MITK; removed MITK (v2021.02).
Fri, Feb 12, 12:11 PM · MITK
kalali edited projects for T26754: Review checklists, added: Next Milestone; removed MITK (v2021.02).
Fri, Feb 12, 11:51 AM · Next Milestone, Restricted Project

Thu, Feb 11

kalali added a comment to T28302: MITK CI jobs for Kaapana.

Following this, are there some requirements that need to be specified here T28280?

Thu, Feb 11, 3:04 PM · CI, MITK

Feb 5 2021

kalali placed T28265: [Checklist] Overhaul ViewNavigator checklists to be in line with the latest changes to the checklists up for grabs.
Feb 5 2021, 11:40 AM · MITK
kalali placed T26485: PACS mode is active while segmentation is drawn up for grabs.
Feb 5 2021, 11:39 AM · Next Milestone, Request for Discussion, MITK
kalali placed T25056: Refactor data manager context menu up for grabs.
Feb 5 2021, 11:14 AM · Noteworthy, MITK
kalali placed T25643: Context menu adds its default actions multiple times up for grabs.
Feb 5 2021, 11:14 AM · MITK

Feb 3 2021

kalali triaged T28270: Segmentation masks not displayed in 3D render window as Normal priority.
Feb 3 2021, 2:18 PM · MITK
kalali edited projects for T19522: Segmentation not displayed in 3d-render window, added: MITK; removed Request for Discussion, MITK (v2021.02).
Feb 3 2021, 2:17 PM · MITK, Bugzilla
kalali changed the status of T19522: Segmentation not displayed in 3d-render window from Resolved to Invalid.
Feb 3 2021, 2:17 PM · MITK, Bugzilla
kalali closed T19522: Segmentation not displayed in 3d-render window as Resolved.

We discussed this and decided to open a new task to cleanly define the problem. We thought that this task mixes many different things without stating the minimal steps to reproduce a single problem, so please continue here: T28270

Feb 3 2021, 2:16 PM · MITK, Bugzilla
kalali created T28270: Segmentation masks not displayed in 3D render window.
Feb 3 2021, 2:16 PM · MITK
kalali added a comment to T19522: Segmentation not displayed in 3d-render window.

I don't mind, I'm not planing to fix this before the release, so if you have time. I'm testing this with the develop branch and comparing it with the MITK 2018 installer.

Feb 3 2021, 12:58 PM · MITK, Bugzilla

Feb 2 2021

kalali placed T28256: Auto-selection preference for Segmentation View was hijacked for something else up for grabs.

Ok, I withdraw from this for now. It is useless to fix this since both views are basically the same but their implementation is different (some things are copied, others aren't). Before putting any effort into this I refer to T28142 and propose to refactor the whole thing after the release.

Feb 2 2021, 10:18 PM · Next Milestone, MITK
kalali claimed T28256: Auto-selection preference for Segmentation View was hijacked for something else.
Feb 2 2021, 1:56 PM · Next Milestone, MITK
kalali placed T28250: [LevelWindowManager] Different behavior in AutoTopMost case and fallback case up for grabs.
Feb 2 2021, 1:38 PM · Next Milestone, MITK
kalali added a comment to T28256: Auto-selection preference for Segmentation View was hijacked for something else.

I tested it and now this explains T27498#217602.

Feb 2 2021, 1:06 PM · Next Milestone, MITK
kalali added a project to T19522: Segmentation not displayed in 3d-render window: Request for Discussion.
In T19522#68902, @goch wrote:

Specifically it is not visible on the 2D planes in the 3D render window, this error is unrelated to volume rendering.

Feb 2 2021, 12:51 PM · MITK, Bugzilla
kalali edited projects for T28246: Create UI test for LevelWindow QtWidgets, added: MITK, Next Milestone; removed MITK (v2021.02).
Feb 2 2021, 10:21 AM · Next Milestone, MITK
kalali placed T28246: Create UI test for LevelWindow QtWidgets up for grabs.
Feb 2 2021, 10:21 AM · Next Milestone, MITK

Feb 1 2021

kalali added a comment to T28262: TimeGeometry inconsistent documentation and implmentation of time bounds and checks.

Since we are supporting multiple images in a single scene. These images can have different time bounds and their time steps can be discretized differently. So even if you have kind of matching dynamic images but one image specifies its acquisition times at 2, 12, 22ms seconds, and the other one at 0, 10, and 20ms, you would have a very sparse discrete time line and only see either no image or at maximum a single image, but never both at the same time. So it is a pretty solid and natural assumption to define timesteps to have a duration until the next time step of the same image, if not explicitly specified otherwise. However, we also have many images that do not have time bounds stored in their files at all (in particular static images) and we need to come up with something completely artificial. It is a pretty severe issue but luckily is not very present in 99% of workflows as users rarely need to have scenes with different dynamic images aligned perfectly or at least not matching 1:1 on a time step basis instead of true time for their purposes.

It would be overkill but to get things sorted out for everyone MITK is missing a complete sophisticated time-line component were you can arrange images and change their time properties just like every video editing software allows you to do for clips.

Feb 1 2021, 2:11 PM · Next Milestone, MITK, Request for Discussion
kalali added a comment to T27883: [Segmentation] Crash and interpolation issues in static segmentation on reference image with strange arbitrary time geometry (3d+t heart).

I tested again with UltrasoundImages\4D_TEE_Data_MV.dcm and everything seems to work as expected. So this task is only valid for strange arbitrary time geometry, as the title describes it.
So I guess the refactoring done in the segmentation tools changed most of the bugs and we got now down to the problem mentioned in T28262.

Feb 1 2021, 12:45 PM · MITK (v2021.02)
kalali added a comment to T28262: TimeGeometry inconsistent documentation and implmentation of time bounds and checks.

It is philosophical indeed, but how is any of these strategies worse than creating a time step with a duration of 0?

We should keep in mind that the whole concept of duration is purely artefical. There is no duration defined. The only things we know are the very time points where they exist.

Feb 1 2021, 12:36 PM · Next Milestone, MITK, Request for Discussion
kalali moved T28265: [Checklist] Overhaul ViewNavigator checklists to be in line with the latest changes to the checklists from Backlog to Checklists on the MITK (v2021.02) board.
Feb 1 2021, 12:06 PM · MITK
kalali renamed T28265: [Checklist] Overhaul ViewNavigator checklists to be in line with the latest changes to the checklists from [Checklist] R+ViewNavigator checklists' most important test is not functioning and default perspectives' layouts are questionable to [Checklist] Overhaul ViewNavigator checklists to be in line with the latest changes to the checklists.
Feb 1 2021, 12:04 PM · MITK
kalali triaged T28265: [Checklist] Overhaul ViewNavigator checklists to be in line with the latest changes to the checklists as Normal priority.
Feb 1 2021, 12:02 PM · MITK
kalali added a subtask for T28108: [Release Checklists] Prepare release checklists: Unknown Object (Maniphest Task).
Feb 1 2021, 12:02 PM · MITK
kalali updated the task description for T26754: Review checklists.
Feb 1 2021, 11:47 AM · Next Milestone, Restricted Project
kalali updated the task description for T26754: Review checklists.
Feb 1 2021, 11:42 AM · Next Milestone, Restricted Project
kalali added a comment to T28258: [Segmentation] Core dumped at multiple instances while Closing Project.

I have finally found the fix! This bug is due to my GPU driver.
My laptop has an AMD Radeon dedicated GPU and MITK uses it by default for rendering its "Standard Display".
I checked the crash log using Event Viewer and found that atio6axx.dll was the culprit here. This is an AMD driver related DLL file.
I switched the default GPU for Mitk workbench to the onboard integrated graphics and that's it!
Problem solved. I am attaching the working screen recording herewith :-)

Feb 1 2021, 11:24 AM · Missing Info, MITK (v2021.02)
kalali added a comment to T28239: Multilabel Segmentation - 3D Segmentation Confused about required outcome.

If you have suggestions for a better structure, please feel free to add it to T28130. The checklists were not even existing before and my goal was to overhaul all the (multi-)label segmentation checklists to include 4D-data tests. I also strove for consistency throughout all checklists.
I see that the bold written statement reads as a new test - that could be changed. However, the test right before already dealt with 4D image data (4D Bild als Testdatensatz) so I assumed it was clear that the 3D-data tests were already finished.
I will also think about some rephrasing / different text format.

Feb 1 2021, 10:48 AM · MITK-ProjectTemplate, MITK (v2021.02)
kalali added a comment to T28250: [LevelWindowManager] Different behavior in AutoTopMost case and fallback case.

I don't know what the real world scenario is to change the Image Rendering Mode, but basically you just have to perform step 8 and 9 to see the bug (step 10).
I could imagine the Image Rendering Mode being changed to either LookupTable_Color or ColorTransferFunction_Color by a line of code inside a module or plugin, which would then make this bug appear, if the auto topmost mode was disabled.

Feb 1 2021, 10:38 AM · Next Milestone, MITK

Jan 30 2021

kalali added a comment to T28254: [Multilabel 2D segmentation] Correction Tool.

I think there was a decision to drop the correction-tool as it is obviously not nice to work with (see https://phabricator.mitk.org/D459#14092).

Jan 30 2021, 9:00 PM · MITK (v2021.02)

Jan 29 2021

kalali updated the task description for T28250: [LevelWindowManager] Different behavior in AutoTopMost case and fallback case.
Jan 29 2021, 8:18 PM · Next Milestone, MITK
kalali triaged T28250: [LevelWindowManager] Different behavior in AutoTopMost case and fallback case as Unbreak Now! priority.
Jan 29 2021, 8:17 PM · Next Milestone, MITK
kalali triaged T28246: Create UI test for LevelWindow QtWidgets as High priority.
Jan 29 2021, 7:14 PM · Next Milestone, MITK
kalali raised a concern with rMITK8ebd602023cf: Fixed gcc compile errors.

There seems to be a bug inside the condition of void QmitkOtsuTool3DGUI::OnSpinboxValueAccept(), see T28243.

Jan 29 2021, 7:01 PM
kalali raised a concern with rMITK34fd4b11f4d8: Fixed review remarks.

There seems to be a bug inside the condition of void QmitkOtsuTool3DGUI::OnSpinboxValueAccept(), see T28243.

Jan 29 2021, 7:01 PM
kalali updated subscribers of T28243: [Segmentation] 3D Otsu does not show preview for a second time.

I remember that I had a discussion about this with @floca, he recently did a lot of changes to the seg tools: https://phabricator.mitk.org/D450?vs=on&id=2056#change-lAwYLYHZrN5g
Here he added a condition to only calculate a preview if some settings have changed. Maybe there was a property missing? (check esp. lines 77, 78, 79 in void QmitkOtsuTool3DGUI::OnPreviewBtnClicked()).

Jan 29 2021, 6:55 PM · MITK (v2021.02)
kalali added a comment to T28242: Live Wire Segmentation bug.

I see your point. The exact task I used is not a duplicate but we discussed this problem with deactivating the tool inside the mentioned task (and you already suggested to fix the checklist). So I get why this task was not found in the first place.

Jan 29 2021, 6:49 PM · MITK-ProjectTemplate, MITK (v2021.02)
kalali merged task T28242: Live Wire Segmentation bug into T28113: [Segmentation] LiveWire tool confirms segmentation upon tool or label change.
Jan 29 2021, 6:11 PM · MITK-ProjectTemplate, MITK (v2021.02)
kalali merged T28242: Live Wire Segmentation bug into T28113: [Segmentation] LiveWire tool confirms segmentation upon tool or label change.
Jan 29 2021, 6:11 PM · MITK
kalali added a comment to T27883: [Segmentation] Crash and interpolation issues in static segmentation on reference image with strange arbitrary time geometry (3d+t heart).

The last thing that happens is a crash.

Jan 29 2021, 3:59 PM · MITK (v2021.02)
kalali added a comment to T27883: [Segmentation] Crash and interpolation issues in static segmentation on reference image with strange arbitrary time geometry (3d+t heart).

Still valid - although it was not clearly defined what happened. Sorry, too many things going on at the same time. I will add a video to show some strange behavior.

Jan 29 2021, 3:36 PM · MITK (v2021.02)
kalali added a comment to T28239: Multilabel Segmentation - 3D Segmentation Confused about required outcome.

That's exactly what I wrote and defined in the checklist. The checklist is correct as it perfectly reflects what's happening in the workbench. This is - as described in the title of the corresponding section - valid for 4D test data.

Jan 29 2021, 2:02 PM · MITK-ProjectTemplate, MITK (v2021.02)

Jan 28 2021

kalali added a comment to T28204: Refactor LevelWindowManagerTest.

I opened a review for my modifications / suggestions for a LevelWindowManagerTest. Please have a look at it: D461
I have explicitly two problems with the current test:

  1. I need to load the three images / datasets for each tests since it is not possible to keep those images in memory for every new tests. Does anyone know how to solve this problem?
  2. I randomly get a failed test in line 287 / 288
m_DataNode2->SetSelected(true);
CPPUNIT_ASSERT_MESSAGE("\"imageForLevelWindow\" property not correctly set", AssertImageForLevelWindowProperty(false, true, false));
Jan 28 2021, 10:28 PM · MITK
kalali added a comment to T28191: Refactor and extend LevelWindow unit tests.

I found several reasons to do a pseudo-UI test so I will come up with a draft for a test of the relevant classes.

Jan 28 2021, 8:36 PM · MITK
kalali moved T26754: Review checklists from Backlog to Checklists on the MITK (v2021.02) board.
Jan 28 2021, 7:51 PM · Next Milestone, Restricted Project

Jan 27 2021

kalali renamed T28203: [Segmentation] 2-d correction tool does not work anymore and should be removed from [Segmentation] 2-d correction tool does not work anymore to [Segmentation] 2-d correction tool does not work anymore and should be removed.
Jan 27 2021, 10:53 PM · MITK (v2021.02)
kalali added a comment to T28203: [Segmentation] 2-d correction tool does not work anymore and should be removed.

Ok, but then we can at least close T22391.

Jan 27 2021, 10:52 PM · MITK (v2021.02)
kalali added a comment to T28191: Refactor and extend LevelWindow unit tests.

Most of the functions that can be called from the QmitkLevelWindowWidget (meaning the slider, the line edit and the contextmenu) are covered in mitkLevelWindowTest.
However, the LevelWindowManager tests where outdated and suboptimal, so I opened T28204.

Jan 27 2021, 6:40 PM · MITK
kalali updated the task description for T28204: Refactor LevelWindowManagerTest.
Jan 27 2021, 6:36 PM · MITK
kalali edited projects for T26754: Review checklists, added: MITK (v2021.02); removed Request for Discussion, MITK.
Jan 27 2021, 6:28 PM · Next Milestone, Restricted Project
kalali updated the task description for T26754: Review checklists.
Jan 27 2021, 6:27 PM · Next Milestone, Restricted Project
kalali added a subtask for T28108: [Release Checklists] Prepare release checklists: Unknown Object (Maniphest Task).
Jan 27 2021, 6:27 PM · MITK
kalali added a subtask for T28108: [Release Checklists] Prepare release checklists: Unknown Object (Maniphest Task).
Jan 27 2021, 6:26 PM · MITK
kalali added a comment to T28203: [Segmentation] 2-d correction tool does not work anymore and should be removed.

Is this obsolete know with the discussion results stated in D459?

Jan 27 2021, 6:21 PM · MITK (v2021.02)
kalali closed T27498: [Selection widgets] Define default for auto selection / listening mechanism as Resolved.
Jan 27 2021, 6:08 PM · Restricted Project, MITK (v2021.02)
kalali triaged T28226: [Semantic relations] Activate auto selection mode per default for the data selection widgets as Normal priority.
Jan 27 2021, 6:07 PM · MITK
kalali moved T27571: Multilabel segmentation does not work with US DICOM images from Backlog to Segmentation on the MITK (v2021.02) board.
Jan 27 2021, 5:59 PM · Missing Info, MITK (v2021.02), Restricted Project
kalali moved T27883: [Segmentation] Crash and interpolation issues in static segmentation on reference image with strange arbitrary time geometry (3d+t heart) from Backlog to Segmentation on the MITK (v2021.02) board.
Jan 27 2021, 5:58 PM · MITK (v2021.02)
kalali moved T28138: [MultiLabel Segmentation] Add tests for the LabelSetImage from Backlog to Segmentation on the MITK (v2021.02) board.
Jan 27 2021, 5:57 PM · MITK
kalali moved T28223: [ImageStatistics] Deleting a datanode after statistics leads to no histogram update for the next node from Backlog to Statistics on the MITK (v2021.02) board.
Jan 27 2021, 5:57 PM · Next Milestone, MITK
kalali moved T28222: [ImageStatistics] Histogram is only shown for timestep 0 from Backlog to Statistics on the MITK (v2021.02) board.
Jan 27 2021, 5:57 PM · MITK (v2021.02)
kalali moved T28221: [ImageStatistics] Histogram is not updated when using ROI from Backlog to Statistics on the MITK (v2021.02) board.
Jan 27 2021, 5:57 PM · MITK (v2021.02)
kalali moved T28203: [Segmentation] 2-d correction tool does not work anymore and should be removed from Backlog to Segmentation on the MITK (v2021.02) board.
Jan 27 2021, 5:56 PM · MITK (v2021.02)