v0.2.3

Various fixes in flowcell map and image stitching.

Version used in STAR Protocol.

What's Changed

• Add mln example by @danilexn in #71

Full Changelog: v0.2.2...v0.2.3

v0.2.2

In flowcell_map, writes the lanes_and_tiles.txt file to the output directory, in case the bcl folder does not have write permission.

v0.2.1

Bugfix when using many cores for flowcell_map

v0.2.0

Changelog

[0.2.0] - 2024-10-03

Added

• New flowcell_map command to convert basecalls from a whole flow cell into barcodes-to-spatial coordinates maps
• Support for bcl-convert in addition to bcl2fastq for demultiplexing
• Added support for the Axio microscope in image_stitch command
• Implemented a more efficient tiling and stitching process for image preprocessing
• Added dnaio dependency for faster FASTQ parsing

Changed

• Updated barcode_preprocessing to handle larger datasets more efficiently
• Improved memory management in various parts of the pipeline
• Refactored pairwise_aligner for better performance and reliability
• Updated segment to use OpenST-specific model directory
• Modified transcript_assign to handle edge cases better
• Improved error handling and logging across the package
• Updated Python version requirement to >3.8 and <3.12

Fixed & Improved

• Corrected issues with coordinate systems in several functions
• Enhanced documentation
• Optimized performance for large dataset processing

v0.1.2

What's changed

• pairwise_aligner: cleanup of cli, does not perform rotation/flipping on image but on ST coordinates (avoid redundant resaving of image). Consider tile bounds when staining image and ST coordinates differ.
• manual_pairwise_aligner: fix rendering depending on threshold, proper flipping for fine alignment. Assign coarse if tile falls outside of image.
• apply_transform: do not perform flipping when supported by < 3 keypoints.

Full Changelog: v0.0.11...v0.1.2

v0.0.11

This release fixes the implementation of openst image_preprocess, and makes models available in bimbstatic (as for our HE_cellpose_rajewsky).