Honeychrome v0.8.3

Honeychrome v0.8.3 Release Notes

We have switched Honeychrome to the LGPL (from GPL) license. As more people try out Honeycrhome and tell us of their interests in contributing to the code or using it for various purposes, we think it's a good time to make this change.
For example, LGPL will allow people to develop their own separate commercial plugins for Honeychrome, while requiring that any developments of the existing code have to be released as open source under the same license.

New features:

• Improved and faster AutoSpectral workflow
• Improved deterination of major (peak) channels in spectral process

Bug fixes:

• Improved compatibility with spectral and conventional cytometers, in particular the FACSDiscover

Additionally the previous v0.8.x Release Notes:

This release contains several new features, improvements and bug fixes.

Major new features

• The two major components of AutoSpectral have been added: Control Cleaning and Autofluorescence. These (optional) enhancements of the unmixing workflow are rapidly becoming the standard tool for fixing unmixing artifacts caused by variable autofluorescence.
• tabbed plugin system: Honeychrome now automatically loads plugins from a plugins folder; two example plugins included. Note that plugins are currently only available if Honeychrome is run in the Python environment (see installation instructions), not as a precompiled executable.
• 2D plots can now be shown as dot plots coloured by gate
• debug data: Honeychrome can send error/crash data if allowed by the user. Note that no personal identifiable information is collected or sent.
• Added support for FCS files for the following spectral cytometers:
  ** Cytek Aurora & Northern Lights
  ** Sony ID7000
  ** BD FACSDiscover A8 & S8
  ** BD FACSymphony A5SE
  ** Beckman Coulter CytoFLEX mosaic
  ** ThermoFisher Attune Xenith
  ** NovoCyte Opteon

PyPi release

• You can now use Honeychrome in a Python environment, simply by issuing the command: "pip install honeychrome", then run "honeychrome" from the command line

Numerous improvements, including the following

• automatic recognition of antigens and fluorophore names in the spectral model editor
• better colourmap ranges to avoid saturation
• imported FCS files can now live anywhere: if they are not in the experiment folder, a symbolic link is set up from the experiment folder, so no more broken relative paths
• build system now produces executable installers for Linux (Ubuntu > 24.04), Windows (10, 11), and MacOs (ARM). Hopefully this will now cover (almost) everyone who had trouble running the previous executables

Also numerous bug fixes.