Mark Eastwood
Mark Eastwood
This PR adds some enhancements to storage.py that are useful when using an AnnotationStore for visualization purposes. Main changes: Support for adding annotations from a hovernet-style .dat through a utility...
This PR adds an AnnotationStoreReader class that allows an annotation store to be read as if it were a WSI. That can be used wherever a WSIreader can be used....
This PR adds in a feature from the most recent version of TIAViz to allow a .csv to be provided in the slides folder that can contain slide level predictions...
### Software versions Python version : 3.10.13 (main, Sep 11 2023, 13:44:35) [GCC 11.2.0] IPython version : 8.18.1 Tornado version : 6.3.3 Bokeh version : 3.4.0 BokehJS static path :...
Initial draft implementation of multi-channel reading.  Still needs lots of work so its a draft at the moment. to do: - [x] test on other examples - [ ]...
This PR is something i've been thinking about from a conversation with Daan when he was here from Radboud doing a seminar a while back. His comment was that one...
This PR is a rough draft of code to allow a registration transform to be loaded as an 'overlay', which will allow the slide to be viewed as if that...
This PR makes a collection of changes related to reviewer comments in the TIAViz paper. Main changes are: 1. Layer names in the interface for static image overlays now are...
Fixes the error related to zarr.errors.FSPathExistNotDir It doesnt exist anymore since zarr v3.0.0, which instead just raises a standard FileNotFoundError rather than checking for different error types in different versions...
This PR takes the sam-viz PR and fixes and substantially simplifies it. I think the original PR was going for a more general prompt segmentor engine that would in theory...