v0.14.25

webknossos

Added

• Added support for new voxel size that stores unit and updated to WEBKNOSSOS API version 7. #1136

v0.14.24

webknossos

Added

• Added an implementation of padded_with_margins for NDBoundingBox class. #1120
• Added a new method add_nx_graphs to skeleton.py which supports to add nx.Graphs to the Skeleton object. #1130

Changed

• Removed additional logging messages during image conversion. #1124

Fixed

• Fixed an issue where cube jobs upsampling, downsampling and compress failed when performed on more than 3 dimensions. #1095
• Fixed an issue where webknossos libs crash when installed with minimal dependencies. #1104

v0.14.23

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

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
• Added .ims as supported suffix. #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
• Added suport for setting a default ID mapping for segmentation layers. 1118

Changed

• Moved functional parts of merge volume annotation CLI to Dataset and Annotation classes. #1055
• Set a new max value for test_align_with_mag_against_numpy_implementation to avoid failures due to high numbers. #1082
• Updated dependabot.yml #1087
• Make lookup for supported suffixes case-insensitive. #1100

Fixed

• Fixed an issue with downloading annotations through the Command Line Interface. #1083

v0.14.22

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

v0.14.21

webknossos

Changed

• Added layer_name as optional argument to Dataset.from_images method. If the created dataset contains only a single layer, layer_name is used, otherwise the given layer_name is a common prefix for all layers. 1054
• The context variable of View.get_buffered_slice_writer() is a BufferedSliceWriter now instead of a Generator. Interaction with the SliceWriter does not change, but updating the offset after first initialization is possible now. 1052

v0.14.20

webknossos

Changed

• Updated ruff to v0.4.0 1047
• Added NIfTI suffix .nii to list of supported bioformats suffixes. #1048

cluster_tools

Changed

• Array jobs are spawned faster now, because common meta data is not serialized for each subjob. The performance improvement is especially big, when custom logging code is configured for array jobs. #1042
• Updated ruff to v0.4.0 1047

v0.14.19

webknossos

Changed

• Removed special CLI command for cubing Nifti files. Use regular conversion command instead. Further, moved Python dependencies for examples and dev dependcies into optional groups which are not installed by default. Install with poetry install --with dev --with examples. #1024

cluster_tools

Changed

• Moved the dependencies for Kubernetes and Dask support into optional extras that need to be installed separately. Either with poetry install --all-extras or pip install -e "all". #1024

v0.14.18

webknossos

Fixed

• Fixed a bug, where using an unaligned topleft value for add_layer_from_images leads to corrupted data. #1036

v0.14.17

webknossos

Changed

• The characters @ and $ are allowed within layer names now. #1034

v0.14.16

webknossos

Added

• Add CLI tool for offline merging of zip annotations with fallback datasets. #996
• Added support for converting new file formats such as DICOM, using the bioformats reader. #1014

Changed

• The rules for naming the layers have been tightened to match the allowed layer names on webknossos. #1016
• Replaced PyLint linter + black formatter with Ruff for development. #1013
• The remote operations now use the WEBKNOSSOS API version 6. #1018
• The conversion of 4D Tiff files to a Zarr3 Dataset is possible. NDBoundingBoxes and VecInt classes are introduced to support working with more than 3 dimensions. #966

cluster_tools

Changed

• Replaced black+isort formatters and pylint linter with ruff. #1023