Ashlar

Bugfixes
* Work around pyjnius mishandling of bool args by jmuhlich in https://github.com/labsyspharm/ashlar/pull/118
(Fixes the error `TypeError: Invalid instance of 'java/lang/Integer' passed for a 'java/lang/Boolean'` when using pyjnius>=1.4)

**Full Changelog**: https://github.com/labsyspharm/ashlar/compare/v1.15.0...v1.15.1

New features
* OME-TIFF files written by Ashlar conform to the [official OME-TIFF pyramid specification](https://docs.openmicroscopy.org/ome-model/6.0.0/ome-tiff/specification.html#sub-resolutions) rather than the unofficial interim pyramid format previously written. (93)
* The `-o` argument supersedes the `-f` and `--pyramid` arguments by allowing the destination filename and format to be included in the path. For example, `-o /path/to/output.ome.tif` will write an OME-TIFF pyramid at the given location, (93)

Bugfixes and other improvements
* Keep the JVM heap (used by the BioFormats file reader) from growing too much (114)
* Memory usage is dramatically reduced. The current usage is the total size of the first cycle's reference channel tiles plus a fixed overhead of about 400 MB.

**Full Changelog**: https://github.com/labsyspharm/ashlar/compare/v1.14.1...v1.15.0

What's Changed
* Fix parsing of channel in filenames by jmuhlich in https://github.com/labsyspharm/ashlar/pull/112
* Website updates by jtefftHiTS

New features
* Added `--flip-mosaic-x` and `--flip-mosaic-y` arguments to allow flipping output mosaic image. (90)

Internal enhancements
* Update README to include `--flip-x` and `--flip-y` arguments in the usage summary and refresh the installation instructions. (83, 89)
* Allow `ashlar.reg.plot_*` functions that can display the stitched image to use a downsampled image. This makes these functions practical for large images which would cause `matplotlib.imshow` to struggle. (86)
* The `preview_slide` script now downsamples images by a factor of 10 by default for improved performance. The factor can be adjusted with the `-d` argument. (86)

New features
* FileSeriesReader adds new parameters `layout` and `direction`. Layout can be set to `raster` (default) or `snake`. Direction can be set to `horizontal` (default) or `vertical`. (76)

Internal enhancements
* Add layer quality plot `ashlar.reg.plot_layer_quality`. (81)

Bug fixes
* Pin random state by default for reproducible stitching results. (77)
* Multi-tile .CZI files and .CZI files with extra images (such as slide labels) are now read correctly. (80)
* Catch rare error caused when assembling mosaic. (79)