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@petebankhead petebankhead released this 09 Jun 15:14
· 51 commits to main since this release
v0.3.1
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Learn about vigilant mode.

This version of qupath-extension-stardist is designed to work with QuPath v0.3.x (and possibly later versions).

It addresses several issues:

  • Invalid operation for scaling (#17)
  • QuPath with CUDA doesn’t release GPU memory after StarDist segmentation Usage & Issues qupath (#11)
    • You'll need to add stardist.close() at the end of any scripts (assuming you've used stardist as the variable name, as it is here)
  • Reduces some occurrences of the dreaded TopologyException
    • More will hopefully be removed in the next main QuPath release

Installation

Install by dragging onto the main QuPath window.

If you installed an older version of the extension, you will need to remove this manually from your extensions folder.

You can find the location by going to Extensions → Installed extensions and expanding any StarDist entry you find. Double-clicking on the path should open the folder that contains the extension.

Tip

When TopologyException does still strike, adding

org.locationtech.jts.geom.GeometryOverlay.isOverlayNG = true

may be a quick scripting hack to overcome it, see https://forum.image.sc/t/stardist-error-message-topologyexception/67708/7

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