2024.9.1

Misc

• Add license
• Fix channel name multiplexer function
• Workaround memory leak when assembling full image

Full Changelog: v2024.4.1...v2024.9.1

2024.4.1

Full Changelog: v2023.9.2...v2024.4.1

2023.9.2

Major

• Add prototype of multi-object aligner.

  1. Coarse align
  2. Segment objects (multiple pieces of tissues)
  3. Fine alignment for each object

• Test image flipping and intensity inversion and use the configuration with the most number of matches

Minor

• Improve feature matching plotting and use absolute thumbnail size in align_he qc output

2023.8.2

Major

• Fix dark grid line due to border/edge effect identified in #10

Improvement

• Use absolute path in CLI script

Full Changelog: v2023.8.1...v2023.8.2

2023.8.1

What's Changed

Major

• Add multi-resolution aligner
• Improve get_aligner convenient function
• Parse pixel size from the image file using ome-types and convert to µm with pint

Improvement

• Allow property overwrite when write pyramid
• Make reader pickle-able
• Skip phase registration if one of the images is blank
• Add extract-channel-write-as-pyramid script
• Lower RAM usage when assembling channels by write to a zarr intermediate

---

• Multi-resolution alignment by @Yu-AnChen in #11
  Full Changelog: v2023.5.2...v2023.8.1

2023.5.2

Major

• Use cv2 for downscale local mean computation
• Read channel image via zarr api when generating pyramid

Minor

• Move pyramid.normalize_mosaics into the pyramid writing function
• Fix tqdm progress bar (workaround)
• Add pyramid_tools script

Full Changelog: v2023.5.1...v2023.5.2

2023.5.1

• Add flow-field script
• Add script for same section H&E registration
• Fix bugs (0e6f0b1)

Full Changelog: v2023.1.1...v2023.5.1

2023.1.1

Major

• Add helper functions to simplify Aligner construction (26b0b60)
  • Pixel size matching when choosing thumbnails
  • Manual set reader pixel size (387a64a)
• Try different moving image orientations and use the one with max number of matches (d46e17a)
• Can use compression when writing to disk (40861a9)

Misc

• Add utility function to generate grid labeled mask and handle mask downsample
• Misc improvements (cfbad15, 7c01725, 7c81c9e)
• Viz computed shifts (9187df6)

2022.9.1

• Move openslide import into SvsReader init

Full Changelog: v2022.8.2...v2022.9.1

2022.8.2

Major

• Un-pin dependencies for better compatibility
• Add imagecodecs (#6)

Full Changelog: v2022.8.0...v2022.8.2