Changelog

Version 0.3.2.rc1

  • Small typos in documentation
  • CI pipelines

Version 0.3.1

  • Documentation

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

  • Initial release

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