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Expected behavior
It's possible to transfer the cell nucleus and cell boundary to ImageJ for use with the macro runner.
Possibly this should also pay attention to the OverlayOptions in the viewer by default... but this is questionable as it introduces a dependency on the viewer settings.
Desktop (please complete the following information):
OS: All
QuPath Version: v0.5.1 (and earlier)
Additional context
The issue relates to OverlayOptions not being passed through, as shown at
petebankhead
changed the title
ImageJ macro runner can't transfert include cell nuclei & boundaries
ImageJ macro runner can't transfer include cell nuclei & boundaries
May 10, 2024
A step towards fixing qupath#1522
Incomplete, because it behaves inconsistently depending upon whether the macro is being run on a selected object or across all annotations / TMA cores. In the first case, the `ImageDisplay` and `OverlayOptions` may be used, but in the second case they are unavailable.
Bug report
Describe the bug
See https://forum.image.sc/t/unexpected-behavior-difference-in-imagej-macro-runner-vs-send-region-to-imagej/96089
Expected behavior
It's possible to transfer the cell nucleus and cell boundary to ImageJ for use with the macro runner.
Possibly this should also pay attention to the
OverlayOptions
in the viewer by default... but this is questionable as it introduces a dependency on the viewer settings.Desktop (please complete the following information):
Additional context
The issue relates to
OverlayOptions
not being passed through, as shown atqupath/qupath-extension-processing/src/main/java/qupath/imagej/gui/ImageJMacroRunner.java
Line 238 in 5066159
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