v0.5.0

What's Changed

• Support for QuPath v0.5.0
• Improved support for TensorFlow via Deep Java Library
• Optionally use the model name for a model stored in the user directory
  • May be in a 'stardist' or 'models' subdirectory
  • Provides an alternative to specifying the full model path
• Reduce non-essential logging messages to 'debug' level

Full Changelog: v0.4.0...v0.5.0

v0.4.0

Main changes

• Support for QuPath v0.4.0 and Deep Java Library (via the Deep Java Library extension)
• Support for initializing the model builder from a Bioimage Model Zoo spec
• Support for preprocessing based upon the full (downsampled) image
  • Fixes #20
• Support for both per-channel and joint channel normalization
  • Fixes #14

The documentation is now here.

v0.3.2

Fixes bug applying detection to a ROI on a z-stack / time series, whereby the default plane would be used for detection (at least if padding > 0).

See https://forum.image.sc/t/cell-detection-with-stardist-on-2d-stack-images/73264/5 for details.

v0.3.1

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

v0.3.0

This version of the QuPath StarDist extension is designed to work with QuPath v0.3.0 (and possibly later versions).

v0.3.0-rc2

This version of the QuPath StarDist extension is designed to work with QuPath v0.3.0-rc2.

It provides a preview before QuPath v0.3.0 is available.