Webknossos

webknossos

Changed
- Updates zarrita to 0.2.7. [1169](https://github.com/scalableminds/webknossos-libs/pull/1169)

webknossos

Fixed
- Add a converter to the VoxelSize field `factor`, to ensure it is a tuple.

webknossos

Added
- Added support for new voxel size that stores unit and updated to WEBKNOSSOS API version 7. [1136](https://github.com/scalableminds/webknossos-libs/pull/1136)

webknossos

Added
- Added an implementation of padded_with_margins for NDBoundingBox class. [1120](https://github.com/scalableminds/webknossos-libs/pull/1120)
- Added a new method add_nx_graphs to skeleton.py which supports to add nx.Graphs to the Skeleton object. [1130](https://github.com/scalableminds/webknossos-libs/pull/1130)

Changed
- Removed additional logging messages during image conversion. [1124](https://github.com/scalableminds/webknossos-libs/pull/1124)

Fixed
- Fixed an issue where cube jobs upsampling, downsampling and compress failed when performed on more than 3 dimensions. [1095](https://github.com/scalableminds/webknossos-libs/pull/1095)
- Fixed an issue where webknossos libs crash when installed with minimal dependencies. [1104](https://github.com/scalableminds/webknossos-libs/pull/1104)

webknossos

Breaking Changes
- Preferring a custom tiff reader over the default PIMS reader to convert tiff files. This change enables the recognition of axis information and the support of tifffiles with more than 3 dimensions. However, it also leads to changed behavior when converting tiff files. Tiffs with axes other than c, x, y, and z, with a shape bigger than 1, are no longer supported for conversion to WKW. Please convert these files to Zarr or Zarr3 Datasets instead. [1043](https://github.com/scalableminds/webknossos-libs/pull/1043)

Added
- Added a pixel level heuristic for distinguishing color and segmentation layers when importing image data with the `from_images` or `add_layer_from_images` method. [1007](https://github.com/scalableminds/webknossos-libs/pull/1007)
- Added .ims as supported suffix. [1085](https://github.com/scalableminds/webknossos-libs/pull/1085)
- Added suffixes supported by bioformats for Zeiss CZI, Leica LOF, Zeiss LSM (laser scanning microscope), Zeiss LSM (Laser Scanning Microscope) 510/710, Leica XLEF and Zeiss AxioVision ZVI (Zeiss Vision Image). [1086](https://github.com/scalableminds/webknossos-libs/pull/1086)
- Added suport for setting a default ID mapping for segmentation layers. [1118](https://github.com/scalableminds/webknossos-libs/pull/1118)

Changed
- Moved functional parts of merge volume annotation CLI to Dataset and Annotation classes. [1055](https://github.com/scalableminds/webknossos-libs/pull/1055)
- Set a new max value for test_align_with_mag_against_numpy_implementation to avoid failures due to high numbers. [1082](https://github.com/scalableminds/webknossos-libs/pull/1082)
- Updated dependabot.yml [1087](https://github.com/scalableminds/webknossos-libs/pull/1087)
- Make lookup for supported suffixes case-insensitive. [1100](https://github.com/scalableminds/webknossos-libs/pull/1100)

Fixed
- Fixed an issue with downloading annotations through the Command Line Interface. [1083](https://github.com/scalableminds/webknossos-libs/pull/1083)

webknossos

Fixed
- Performing `webknossos upload` on a windows machine leaded to loss of directory structure due to backslashes in the relative paths. This was fixed by [1067](https://github.com/scalableminds/webknossos-libs/pull/1067)