Napari-clusters-plotter

Most important changes

Now the labels do not need to be sequential for the visualization to be correct. Thanks to haesleinhuepf!
Two new dimensionality reduction algorithms (Isomap and MDS).

What's Changed
* Fill measurement lists when initializing dock widgets by haesleinhuepf in https://github.com/BiAPoL/napari-clusters-plotter/pull/179
* increase spot alpha by haesleinhuepf in https://github.com/BiAPoL/napari-clusters-plotter/pull/183
* Add more docstrings by lazigu in https://github.com/BiAPoL/napari-clusters-plotter/pull/184
* Make widgets available via public API by lazigu in https://github.com/BiAPoL/napari-clusters-plotter/pull/185
* Add dimensionality reduction algorithms (Isomap and MDS from scikit-learn) by lazigu in https://github.com/BiAPoL/napari-clusters-plotter/pull/187
* Add a check whether given axes names exist when plotting from notebook by lazigu in https://github.com/BiAPoL/napari-clusters-plotter/pull/188
* Set unselected datapoints as background/noise by thorstenwagner in https://github.com/BiAPoL/napari-clusters-plotter/pull/193
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/BiAPoL/napari-clusters-plotter/pull/201
* add force redraw option by thorstenwagner in https://github.com/BiAPoL/napari-clusters-plotter/pull/199
* Support non sequential label images and unsorted measurements by haesleinhuepf in https://github.com/BiAPoL/napari-clusters-plotter/pull/197
* Use unique elements of cluster IDs to create colormap by thorstenwagner in https://github.com/BiAPoL/napari-clusters-plotter/pull/203
* Update codecov.yml by lazigu in https://github.com/BiAPoL/napari-clusters-plotter/pull/208
* Update requirements.txt by lazigu in https://github.com/BiAPoL/napari-clusters-plotter/pull/210
* Fix axes labels not displayed bug by lazigu in https://github.com/BiAPoL/napari-clusters-plotter/pull/194

New Contributors
* thorstenwagner made their first contribution in https://github.com/BiAPoL/napari-clusters-plotter/pull/193

**Full Changelog**: https://github.com/BiAPoL/napari-clusters-plotter/compare/0.6.1...0.6.2

Bugfixes
* UMAP crashing jupyter notebook kernel is fixed by disabling multithreading for this algorithm
* Fixed a bugfix (keyerror) related to the newest Matplotlib version

What's Changed
* Update installation instructions in the readme by lazigu in https://github.com/BiAPoL/napari-clusters-plotter/pull/162
* Disable one test that passes locally but timeout error on github by lazigu in https://github.com/BiAPoL/napari-clusters-plotter/pull/166
* Update menu locations in docs by haesleinhuepf in https://github.com/BiAPoL/napari-clusters-plotter/pull/165
* Create codecov.yml by lazigu in https://github.com/BiAPoL/napari-clusters-plotter/pull/173
* Disable multithreading for UMAP by lazigu in https://github.com/BiAPoL/napari-clusters-plotter/pull/170
* Disable buttons when computation is running by lazigu in https://github.com/BiAPoL/napari-clusters-plotter/pull/171
* Remove pinned version of joblib by lazigu in https://github.com/BiAPoL/napari-clusters-plotter/pull/174
* UMAP/t-SNE dimensions by lazigu in https://github.com/BiAPoL/napari-clusters-plotter/pull/172


**Full Changelog**: https://github.com/BiAPoL/napari-clusters-plotter/compare/0.6.0...0.6.1

Major updates

* The measurements widget is no longer a part of the plugin. It is recommended to use either [napari-pyclesperanto-assistant](https://www.napari-hub.org/plugins/napari-pyclesperanto-assistant) or [napari-skimage-regionprops](https://www.napari-hub.org/plugins/napari-skimage-regionprops) to derive measurements from labelled images. Thus, the [pyclesperanto_prototype](https://github.com/clEsperanto/pyclesperanto_prototype) is no longer a dependency of the plugin. Now it is optional, and if installed "clusters IDs in space" generation is GPU-accelerated.
* Major code reorganisation to separate all the Qt code. Frontend did not change.

What's Changed
* Change saved axes labels color by lazigu in https://github.com/BiAPoL/napari-clusters-plotter/pull/130
* Get rid of pyclesperanto dependancy by Cryaaa in https://github.com/BiAPoL/napari-clusters-plotter/pull/140
* Un spaghettifying Qt code by Cryaaa in https://github.com/BiAPoL/napari-clusters-plotter/pull/117
* Add the plotter to measurement tool menu AND visualization tool menu by Cryaaa in https://github.com/BiAPoL/napari-clusters-plotter/pull/142
* Remove plugin preview by haesleinhuepf in https://github.com/BiAPoL/napari-clusters-plotter/pull/147
* Uncomment dim reduction tests by lazigu in https://github.com/BiAPoL/napari-clusters-plotter/pull/150
* Change pypi badge to conda one by lazigu in https://github.com/BiAPoL/napari-clusters-plotter/pull/152
* Fix a couple of small bugs by lazigu in https://github.com/BiAPoL/napari-clusters-plotter/pull/155
* Update readme by lazigu in https://github.com/BiAPoL/napari-clusters-plotter/pull/156

**Full Changelog**: https://github.com/BiAPoL/napari-clusters-plotter/compare/0.5.2...0.6.0

What's Changed
* update __version__ by haesleinhuepf in https://github.com/BiAPoL/napari-clusters-plotter/pull/111
* Create CITATION.cff by lazigu in https://github.com/BiAPoL/napari-clusters-plotter/pull/121. It is now possible to cite the repository from the "about" section in the sidebar.
* Fixing scale inheritance by Cryaaa in https://github.com/BiAPoL/napari-clusters-plotter/pull/124. The scaling of the original labels layer is now inherited by the "cluster_ids_in_space" layer. Thanks to Michael-L-Miller for reporting!
* Add perplexity check, fix test by lazigu in https://github.com/BiAPoL/napari-clusters-plotter/pull/128. Chosen perplexity value is now automatically checked and the widget indicates in red if the chosen value is incorrect.
* remove constraint for python version < 3.10 by haesleinhuepf in https://github.com/BiAPoL/napari-clusters-plotter/pull/127. Thanks to jaimergp for spotting!

**Full Changelog**: https://github.com/BiAPoL/napari-clusters-plotter/compare/0.5.1...0.5.2

New Features
* Timelapse functionality is extended to tracking data: tracking timelapse data automatically detected when using 4D images and measurements without a column named "frame"

What's Changed
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/BiAPoL/napari-clusters-plotter/pull/96
* Increase code coverage: Making tests for plotter utilities by Cryaaa in https://github.com/BiAPoL/napari-clusters-plotter/pull/101
* Bugfix: Fix the license file by haesleinhuepf in https://github.com/BiAPoL/napari-clusters-plotter/pull/99
* adding acknowledgements to readme by haesleinhuepf in https://github.com/BiAPoL/napari-clusters-plotter/pull/102
* Improve documentation: add quick links to readme by lazigu in https://github.com/BiAPoL/napari-clusters-plotter/pull/106
* Bugfix: fix tests by haesleinhuepf in https://github.com/BiAPoL/napari-clusters-plotter/pull/109
* Bugfix: don't redraw plot in case the plot is invisible by haesleinhuepf in https://github.com/BiAPoL/napari-clusters-plotter/pull/108
* Reintroduction of feature: make option to have tracking data to plot by Cryaaa in https://github.com/BiAPoL/napari-clusters-plotter/pull/105


**Full Changelog**: https://github.com/BiAPoL/napari-clusters-plotter/compare/0.5.0...0.5.1

New Features
* Timelapse support for:
- Measurements: automatically detects timelapse data as shape (time, z, y, x) for 3D data and (time, z =1, y, x) for 2D data
- Plotting: datapoints of current frame highlighted in plot, plotting features against frame is possible.
* Plotting point sizes and transparency dynamically change with number of datapoints
* Properties are auto updated in the plotting, clustering and dimnensionality reduction algorithms


What's Changed
* Timelapse support by Cryaaa and lazigu in https://github.com/BiAPoL/napari-clusters-plotter/pull/77
* bugfix: remove layer interactivity and restore zoom/pan/tilt by haesleinhuepf in https://github.com/BiAPoL/napari-clusters-plotter/pull/80
* Added troubleshooting information for Mac users by jo-mueller in https://github.com/BiAPoL/napari-clusters-plotter/pull/87
* Auto update properties in widgets by Cryaaa in https://github.com/BiAPoL/napari-clusters-plotter/pull/91


**Full Changelog**: https://github.com/BiAPoL/napari-clusters-plotter/compare/0.4.0...0.5.0