v1.3.1

Version 1.3.1 [11/03/2026]

This release makes changes to aspects of the pipeline structure, unifying pre-processing. It also adds a little more output from the final report.

Added

• Added the PREPROCESSIMAGE process, which unifies pre-processing and marker selection, so that inputs for all downstream processes are normalised.
• Added CSV outputs from the R report which has mean marker intensity per cluster for each resolution of clustering.

Changed

• Updated marker matching logic to be more precise:
  • Marker names are matched token-wise with complete matches preferred to token matches (which are preferred to partial matches).
• Marker file no longer forbids spaces in marker names
• Updated documentation to reflect changes to inputs and outputs.

Removed

• Removed the HANDLESTITCHED process
• Removed the SEPARATEIMAGECHANNELS process and associated scripts

v1.3.0

Version 1.3.0 [27/02/2026]

This is the first official release of mihcro! Thanks to all the contributions that have gotten the pipeline to where it is now!

Added

• Enabled membrane channel extraction and use in segmentation
• Added parameterisation for Cellpose process, including:
  • Specification of custom models
  • Specification of cell diameter
• Added a local copy of cyto3 in bin/ to reduce runtime with cellpose
• Added a resegmentation script (under assets/helper_scripts/cellpose_resegmentation) to streamline Cellpose model retraining

Changed

• Changed the repository name - introducing mihcro!
• Made several changes to the downscaling process for accuracy and efficiency
• Better handling of the marker file input, including oddly-named markers and unused markers
• Streamlined QC Report and added down-sampling for clustering to improve runtime when data has too many cells.
• Fixed a few nagging issues with handling of inputs, allowing for more flexibility in the samplesheet
• Altered the structure of outputs from the pipeline, organising them more intuitively. '
• Updated diagram, citations and credits in the READMEs.

v1.2.0-dev

Version 1.2.0-dev [30/10/2025]

Added

• Added report output for the last step of analysis, replacing the old scimap step. Analysis is now rendered by R into a convenient HTML.
• Added preview rendering for segmentation output, enabling manual inspection of segmentation boundaries.
• Added an optional DAPI pre-processing step, featuring background removal and Otsu thresholding for binarisation, with the aim to make segmentation processes more efficient.

Changed

• Expanded README.md, and fleshed out outputs.md and usage.md for clearer documentation overall.
• Altered several modules to use the same containers where possible, to reduce the number of containers being downloaded.

v1.1.0-dev

Version 1.1.0-dev [15/10/2025]

Added

• Selection of segmentation method as a parameter.
• Altered workflow to handle pre-stitched or legacy HALO tiff inputs.
• Added a downscaling step which reduces resolution to 1px/um for faster segmentation.
• Expanded README and added a metro diagram.

Fixed

• Fixed a bug where warnings were exported into tiff metadata xml.