Palom

**Full Changelog**: https://github.com/labsyspharm/palom/compare/v2023.9.2...v2024.4.1

Major

- Add prototype of multi-object aligner.
1. Coarse align
1. Segment objects (multiple pieces of tissues)
1. 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

Major

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

Improvement

- Use absolute path in CLI script

**Full Changelog**: https://github.com/labsyspharm/palom/compare/v2023.8.1...v2023.8.2

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 https://github.com/labsyspharm/palom/pull/11
**Full Changelog**: https://github.com/labsyspharm/palom/compare/v2023.5.2...v2023.8.1

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**: https://github.com/labsyspharm/palom/compare/v2023.5.1...v2023.5.2

- Add flow-field script
- Add script for same section H&E registration
- Fix bugs (0e6f0b1e844c7e3e21ffbc187ac88942a0983e52)


**Full Changelog**: https://github.com/labsyspharm/palom/compare/v2023.1.1...v2023.5.1