Changelog
Version 0.3.2.rc1
- Small typos in documentation
- CI pipelines
Version 0.3.0
- Separate miscmics package for easier processing of resulting file in external scripts
- Pinned versions
- Minor Bugfixes
- Install bash script icell
Version 0.2.5
- Uniform setter for scalar values to abstract implementation away
- Removed Orange Dropdowns from OrangeWidget. Kept throwing errors in different Orange3 versions
- Accept ‘*.json’ and ‘*.ent’ files
Version 0.2.4
- Better filters for loading dialogs
- Removed unused Inputs and Outputs from Orange3 Widget
- The tags ‘C1’ - ‘C10’ and ‘done’ now have a hardcoded effect on the coloring of segments
- The console script ‘entitycli’ is working now and allows for non-GUI entity manipulation
and extraction of information into various formats
- Shortcut P to print the current channel only as a png file
- Shortcut Y to set the ‘done’ tag for the last active entity (like keys 0-9)
- entitycli can now draw segments by a color scheme
- The features extracted are now a functional mapping
Version 0.2.3
- EntityManager offers two iterations now: Active only or All
- EntityManager can pop entities, analogous to Dict.pop()
- Entities generated from Pixmap are dilated by one pixel upon loading to allow for easy merging
Version 0.2.2
- Segmentation pixmaps can be loaded directly
Version 0.2.1
- Changed to Apache Licence
Version 0.2.0
ViewContext
- Parallel display of multiple channels in a single grid layout view
- Background images can be set for each channel individually, e.g., with multiplexed microscopy images
- The view and mouse is synchronized to show the same image region in each channel
- On-the-fly contrast enhancement of each channel
Sessions
- Multiple ViewContext layouts (channel layout, contrast enhancement) can be stored in a session
- Sessions can be persistently saved and loaded between usage
Entities
- Polygon-based objects that can model e.g. cell segments
- Polygons can be edited/drawn
- Overlap of cells can be modeled
- Tags or scalar values can be assigned to Entities
- InfoBox shows annotations of the entity under the mouse cursor
- Entities can be hidden or shown
- Tag-dependent coloring possible (hardcoded ATM)
- All data can be stored in plain JSON
- Modal editing - switching between Normal - Draw - Erase
Orange3 Add-On
- Integration into Orange3
- Load images using the Orange3-ImageAnalytics add-on
Misc
- Utility script in entitytool to easily work with JSON data
Known Issues
- Occasionally, the view can not be panned anymore using the middle mouse button in draw mode. Switching to select mode and back into draw mode reenables panning again