This release marks the point where the pipeline was moved from labsyspharm/mcmicro over to the new nf-core community, at nf-core/mcmicro.

View the previous changelog at labsyspharm/mcmicro/CHANGES.md

In addition to porting to the new nf-core community, the pipeline has had a number of major changes in this version.

• Input files can live anywhere not necessarily with output files.
• Input formatting is changed from a custom directory structure to a sample sheet see docs.
• No longer need for custom params.yml, now can be passed as command line options or as nextflows -params-file JSON format.
• Added a prelude step that verifies input image metadata and reports inconsistencies/errors.
• Removed unmicst segmenter.
• Added cellpose as the new default segmenter, customized for smaller footprint!
• Basic illumination upgraded to the next generation basicpy tool.

And many performance quirks and bug fixes! We would like to thank everyone involved in this release!