Pete

ShapeReader conversion does not always correctly identify holes

3

_ShapeReader_ can give unexpected (at least to me...) results in some cases, I believe because the assumption within [`isHole(Coordinate[] pts)`](https://github.com/locationtech/jts/blob/bac855f9fe3a75af523b43f95f4b9a09b4ab5359/modules/core/src/main/java/org/locationtech/jts/awt/ShapeReader.java#L115) does not always match the underlying Java AWT representation. Here...

Basically, add this as a built-in command: * https://github.com/qupath/qupath/issues/77#issuecomment-301234930 It isn't a beautiful way to create a manual TMA grid, but it should be better than nothing (or hunting for...

QuPath gets stuck when trying to open an image / opens it at low resolution only

1

## Bug report **Describe the bug** QuPath v0.3.2 hangs when attempting to open certain images with Bio-Formats, outside of a project. The problem occurs when: * Bio-Formats is the reader...

Add text/markdown to objects

3

Support for annotation descriptions is improved in #1004 The screenshots below show the current status. The purpose of this feature request is to discuss further enhancements, in particular: * Consolidating...

Improve dialog that appears on startup

2

## Bug report **Describe the bug** When QuPath is first launched, a few key options are presented to the user - which are currently the memory settings, locale and whether...

QuPath's viewer does not support ICC profiles

2

## Bug report **Describe the bug** QuPath's viewer doesn't (really) support ICC profiles. This makes the display colors inconsistent with that seen in other viewers, for some file formats. **To...

## Bug report **Describe the bug** Initial bug report and steps to reproduce at https://forum.image.sc/t/qupath-script-cannot-access-java-library-and-project-data-simultanely/63388 The problem is that a class cannot be loaded from an extension far for multiple...

Spurious 'Physical memory usage is too high' errors when training a pixel classifier

29

## Bug report **Describe the bug** QuPath sometimes reports OutOfMemoryErrors when training or running a pixel classifier in situations where the memory use is not actually too high. This has...

GPU memory not freed when using OpenCV DNN

2

## Bug report **Describe the bug** GPU memory isn't released when using a `DnnModel` repeatedly. This can be seen when using StarDist. **To Reproduce** See https://github.com/qupath/qupath-extension-stardist/issues/11 Copied here because the...

OpenSlide support in QuPath

11

QuPath supports reading whole slide images using two open source libraries: [Bio-Formats](https://www.openmicroscopy.org/bio-formats/) and [OpenSlide](http://openslide.org). Of these, Bio-Formats is much more extensive and actively-maintained; OpenSlide only really supports single-plane, 8-bit RGB...