v1.19.0

New features

• Update bioformats dependency to 8.0.1 by @jmuhlich in #231
• Now compatible with Python 3.12 (#223)
• Now compatible with scikit-image>=0.20 by @joshua-gould in #215

Bugfixes

• Fix byte order when reading from big-endian formats by @jmuhlich in #230

Other improvements

• Use light gaussian filtering during coarse alignment by @jmuhlich in #214
• Update python+package versions in install instructions by @jmuhlich in #224
• Update versioneer to 0.29 by @jmuhlich in #223

New Contributors

• @joshua-gould made their first contribution in #215

Full Changelog: v1.18.0...v1.19.0

v1.18.0

New features

• Use zlib compression with predictor pre-filter in OME-TIFF output by @jmuhlich in #176, #177
• Add bioformats support to fileseries/filepattern readers by @jmuhlich in #178
• Add --stitch-alpha and --maximum-error args by @jmuhlich in #181
• Add barrel/pincushion correction support by @jmuhlich in #183, #184, #185
• Allow preview_slide to use any image reader (fileseries etc.) by @jmuhlich in b5c261d

Bugfixes

• Small fixes to visualization helpers by @jmuhlich in #175
• Correct handling of linear model fitting failure by @jmuhlich in #187
• Fix errors when stitching synthetic data by @jmuhlich in 387eff5)
• Escape parentheses in fileseries/filepattern pattern by @jmuhlich in #192
• Fix tile size and dtype logic in fileseries and filepattern readers by @jmuhlich in 62fbc42
• Tell Bioformats not to "flatten" pyramids by @jmuhlich in #193
• Fix napari image interpolation argument by @jmuhlich in #182

Other improvements

• Improve coarse-alignment thumbnail quality by @jmuhlich in #180
• Update seaborn JointGrid call to latest API by @jmuhlich in #179
• Update dependencies installed in docker container by @jmuhlich in #186
• Bump nokogiri from 1.13.6 to 1.14.3 in /docs by @dependabot in #189
• Update link to manuscript by @jtefftHiTS in #155

Full Changelog: v1.17.0...v1.18.0

v1.17.0

New features

• Support common RGB image formats like JPEG and PNG in fileseries/filepattern readers by @jmuhlich in #139

Bugfixes

• Fix error in fileseries reader when channel count is not 3 or 4 by @jmuhlich in #136
• Set minimum number of pyramid levels to 1 by @jmuhlich in #137
• Use old normalization method (none) for new scikit-image version of phase cross correlation, to match the old behavior of Ashlar by @jmuhlich in #144
• Account for non-integer relative offsets in LayerAligner by @jmuhlich in #142
• Fix regressions in plates (HTS) mode by @jmuhlich in #149

Other improvements

• Bump tzinfo from 1.2.9 to 1.2.10 in /docs by @dependabot in #145

Full Changelog: v1.16.0...v1.17.0

v1.16.0

General Improvements

• Improve argument parsing and help text by @jmuhlich in #128
• Update scikit-image to 0.19 by @jmuhlich in #130

Full Changelog: v1.15.3...v1.16.0

v1.15.3

Bugfixes

• Tolerate very slightly non-square pixels by @jmuhlich in #123

Full Changelog: v1.15.2...v1.15.3

v1.15.2

Bugfixes

• Fix some bugs in our usage of tifffile by @jmuhlich in #120

Full Changelog: v1.15.1...v1.15.2

v1.15.1

Bugfixes

• Work around pyjnius mishandling of bool args by @jmuhlich in #118
  (Fixes the error TypeError: Invalid instance of 'java/lang/Integer' passed for a 'java/lang/Boolean' when using pyjnius>=1.4)

Full Changelog: v1.15.0...v1.15.1

v1.15.0

New features

• OME-TIFF files written by Ashlar conform to the official OME-TIFF pyramid specification 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: v1.14.1...v1.15.0

v1.14.1

What's Changed

• Fix parsing of channel in filenames by @jmuhlich in #112
• Website updates by @jtefftHiTS

v1.14.0

New features

• Added --flip-mosaic-x and --flip-mosaic-y arguments to allow flipping output mosaic image. (#90)