Scportrait

What's Changed
* Restructure spdata by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/187
* Rename cell id param by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/267
* [FEATURE] rescaling of images contained in spatialdata objects by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/266
* improve plotting capabilities


**Full Changelog**: https://github.com/MannLabs/scPortrait/compare/v1.3.2...v1.3.3

What's Changed
* improve dependencies by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/259
* add additional plotting capabilities to scportrait
* fix small bugs

**Full Changelog**: https://github.com/MannLabs/scPortrait/compare/v1.3.1...v1.3.2

What's Changed
* improve h5sc UI and add plotting capabilities by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/253
* properly preserve channel names when loading from sdata by machth in https://github.com/MannLabs/scPortrait/pull/256
* [VERSION] Bump version to 1.3.1 by github-actions in https://github.com/MannLabs/scPortrait/pull/257


**Full Changelog**: https://github.com/MannLabs/scPortrait/compare/v1.3.0...v1.3.1

What's Changed
* update single-cell image format to utilize AnnData by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/245
* [VERSION] Bump version to 1.3.0 by github-actions in https://github.com/MannLabs/scPortrait/pull/249


**Full Changelog**: https://github.com/MannLabs/scPortrait/compare/v1.2.0...v1.3.0

What's Changed
* [Fixes] Initialize project from spatialdata by lucas-diedrich in https://github.com/MannLabs/scPortrait/pull/146
* Update docs by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/156
* Prevent duplication sdata reader by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/155
* implement automatic workflow for bumping version numbers by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/157
* [VERSION] Bump version to 1.1.1-dev0 (merge after release) by github-actions in https://github.com/MannLabs/scPortrait/pull/161
* update project status tracking by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/152
* add changes from development to main by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/163
* Fix docs by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/164
* fix some small bugs by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/167
* improve spatialdata file handling by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/171
* Improve typehinting and docstrings by Zethson in https://github.com/MannLabs/scPortrait/pull/183
* [FIX] use new centers file naming syntax by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/188
* improve interactive sdata viewing experience by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/189
* Update cellpose version to 3.1.1 by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/197
* replace deprecated imwrite with imsave by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/199
* Improve ml capabilities by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/191
* update Phenix Parser to work with HarmonyV7 by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/206
* set default values for match masking correctly by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/207
* Improve segmentation cellpose by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/210
* ensure that in sharded segmentations results are transferred to spatialdata using memory mapping by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/212
* Ignore mahotas 3.12 SyntaxWarnings by Zethson in https://github.com/MannLabs/scPortrait/pull/213
* Ensure sharding is resolved correctly by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/201
* [FiX] add support for passing config path as PosixPath by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/216
* add workflow to release package on pypi by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/219
* Improve log output during stitching by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/220
* improve handling of empty spatialdata files to make use of overwrite more robust by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/221
* Improve extraction workflow by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/204
* Improve cellpose segmentation documentation by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/225
* add function of writing shape layer by machth in https://github.com/MannLabs/scPortrait/pull/226
* Bump python version3.12 by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/230
* Making contributing to scPortrait easier by namsaraeva in https://github.com/MannLabs/scPortrait/pull/123
* Ensure dtypes are consistent over all image tiles during stitching by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/235
* [FEATURE] add ConvNextFeaturizer by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/238
* Fix parsing by sophiamaedler in https://github.com/MannLabs/scPortrait/pull/234
* Run CI on PRs by Zethson in https://github.com/MannLabs/scPortrait/pull/243
* ADDED: alignment function for DAPI across different cycles by a-o-can in https://github.com/MannLabs/scPortrait/pull/240
* Support numpy 2 by Zethson in https://github.com/MannLabs/scPortrait/pull/144
* Add Multiclass Callback by namsaraeva in https://github.com/MannLabs/scPortrait/pull/246
* [VERSION] Bump version to 1.2.0 by github-actions in https://github.com/MannLabs/scPortrait/pull/247

New Contributors
* lucas-diedrich made their first contribution in https://github.com/MannLabs/scPortrait/pull/146
* machth made their first contribution in https://github.com/MannLabs/scPortrait/pull/226
* a-o-can made their first contribution in https://github.com/MannLabs/scPortrait/pull/240

**Full Changelog**: https://github.com/MannLabs/scPortrait/compare/v1.1.0...v1.2.0

What's Changed
- many bug fixes
- better support of spatial-data format
- code cleanup and implementation of coding best practices

New Contributors
* Zethson made their first contribution in https://github.com/MannLabs/scPortrait/pull/79
* nik-as made their first contribution in https://github.com/MannLabs/scPortrait/pull/89
* MarcMarc94 made their first contribution in https://github.com/MannLabs/scPortrait/pull/110
* github-actions made their first contribution in https://github.com/MannLabs/scPortrait/pull/160

**Full Changelog**: https://github.com/MannLabs/scPortrait/compare/v.1.0.0...v1.1.0