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How to ease the handling of external generated segmentations
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Currently the workbench does not support simple binary segs any more directly (only DICOM Seg and our own multi label nrrds are supported). They have to be converted manually. This could be tedious.

How to make it easier?


  • Command line tool to convert data into multi label seg format
  • python support module
  • offer a reader in case of binary itk images to load as seg
    • as a new reader: convinient, but slows the loading even more as the image has to be interpreted and completly processed on mime type level to decide if the reader should be applied
    • as a new mime type: faster, but not so convinient would enforce a pop up for all supported data formates in order to choose if it should be loaded as image or as segmentation)
  • introduce a hook (at application level (here it could be more general ?!? or seg view level) that monitors the data storage and proposes conversion (or does auto convert as soon as a legacy segmentation is loaded).

Event Timeline

floca moved this task from Backlog to In candidates on the MITK (v2023.04) board.
floca renamed this task from How to easy the handling of external generated segmentations to How to ease the handling of external generated segmentations.Nov 30 2022, 11:14 AM
floca triaged this task as Normal priority.Nov 30 2022, 11:17 AM
floca moved this task from In candidates to Segmentation on the MITK (v2023.04) board.
kislinsk added a subscriber: kislinsk.

Request for Discussion Discussion result:

  • Remove special "binary" flag since we do not support legacy binary images anymore anyways (icon, property, mapper)
  • Somehow make it more convenient to open plain images as segmentations compared to "Convert to Segmentation"

Turned out it is not straight forward to remove the "binary" feature since it is still used in quite a few crucial places like the segmentation paintbrush tool preview.

Is it realy used or just still supported?

is the discussion realy over now? I think this is also more an meta task, concrete actions like removing binary tag and such should be sub tasks.
@kislinsk Could you make sub tasks out of your discussion points. Thanks.