0.8.1

What's Changed

• Fix setting bin number manually by @zoccoler in #325
• Fix color future warning by @zoccoler in #308
• Bump version and automatic version determination by @tsmejkal in #336

New Contributors

• @tsmejkal made their first contribution in #336

Full Changelog: 0.8.0...0.8.1

0.8.0

What's Changed

Support for new napari layers:

• Add support for points layer by @jo-mueller in #256
• Add support for surface layer by @lazigu in #229

Bug Fixes:

• Added explicit dependencies by @jo-mueller in #274
• Fixed link to test badge by @jo-mueller in #278
• Convert max label to integer before using it as parameter for np.zeros by @stefanhahmann in #284
• Fix Tracking Layer by @stefanhahmann in #286
• Fixing the problem of accessing properties in image layers by @Cryaaa in #296
• Fix zooming problem by @thorstenwagner in #298
• Adding another small fix for future warning by @Cryaaa in #309
• Fix bug where some colormaps were not displayed in the historam by @zoccoler in #318
• Prefer loading features from features rather than properties by @jo-mueller in #319

Performance and Enhancements:

• Don't recalculate histogram if not necessary by @thorstenwagner in #282
• Speed-up generate cluster image by @thorstenwagner in #283
• More efficient multiple cluster selection by @thorstenwagner in #287
• Update full data only when data is changed by @thorstenwagner in #288
• Update method generate_cluster_tracks() by @stefanhahmann in #290
• Update axes limits when plotting by @thorstenwagner in #294
• Fix opacity adjustment and set it to low non-zero value by @zoccoler in #280
• Fix labels layer opacity setting and bug when viewer is closed from code by @zoccoler in #313
• Set up automatic deployment by @jo-mueller in #304

Documentation and Code Style:

• Add additional explanation regarding zero as a label by @stefanhahmann in #270
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #252
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #292
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #293
• Add example dataset for tracking data. by @stefanhahmann in #300
• Adding example data and notebooks to load the data by @Cryaaa in #310
• Update doc layer types by @zoccoler in #311
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #312

Tests:

• Add more tests for layers in 3 d/4 d by @zoccoler in #315

New Contributors

• @stefanhahmann made their first contribution in #270

Full Changelog: 0.7.3...0.8.0

0.7.3

What's Changed

• Make cluster image uint32 by @thorstenwagner in #259
• Remove features that contain inf by @zoccoler in #264

Full Changelog: 0.7.2...0.7.3

0.7.2

What's Changed

• Fix reset zoom by @thorstenwagner in #254

Full Changelog: 0.7.1...0.7.2

0.7.1

Bugfix:

• Incompatibility with pytorch on conda-forge/Windows (#248 )

0.7.0

New features

• Use 2D Histogram for visualization by @thorstenwagner in #196
• Colormap pulldown for 2D histogram by @marabuuu in #239
• Implement Histogram1D if the same measurement is selected for both axes by @lazigu and @zoccoler in #237
• Change highlights in timelapse data plotting to brighter colors instead of white by @Cryaaa in #244

What else has changed

• Allow flexible cluster ids by @zoccoler in #205
• Pin numpy version due to incompatibility with numba by @lazigu in #219
• Update tests workflow file (disable tests on windows, update versions, use codecov token) by @lazigu in #231
• Fix small bugs in the plotter widget #2 by @lazigu in #227
• Fixes link of the tests badge by @lazigu in #233
• Don't reset zoom on redraw by @thorstenwagner in #214
• Add more tests by @lazigu in #230
• Update documentation by @lazigu in #234
• Add min distance for UMAP parameter by @lazigu in #235
• Add optional custom name field for dimensionality reduction by @lazigu in #236
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #238
• Implement lowercase interpretation of keys by @Cryaaa in #243
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #240
• make layout slimmer by @haesleinhuepf in #245
• Expose frame_changed method by @zoccoler in #221

New Contributors

• @marabuuu made their first contribution in #239

Full Changelog: 0.6.2...0.7.0

0.6.2

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

New Contributors

• @thorstenwagner made their first contribution in #193

Full Changelog: 0.6.1...0.6.2

0.6.1

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 #162
• Disable one test that passes locally but timeout error on github by @lazigu in #166
• Update menu locations in docs by @haesleinhuepf in #165
• Create codecov.yml by @lazigu in #173
• Disable multithreading for UMAP by @lazigu in #170
• Disable buttons when computation is running by @lazigu in #171
• Remove pinned version of joblib by @lazigu in #174
• UMAP/t-SNE dimensions by @lazigu in #172

Full Changelog: 0.6.0...0.6.1

0.6.0

Major updates

• The measurements widget is no longer a part of the plugin. It is recommended to use either napari-pyclesperanto-assistant or napari-skimage-regionprops to derive measurements from labelled images. Thus, the 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 #130
• Get rid of pyclesperanto dependancy by @Cryaaa in #140
• Un spaghettifying Qt code by @Cryaaa in #117
• Add the plotter to measurement tool menu AND visualization tool menu by @Cryaaa in #142
• Remove plugin preview by @haesleinhuepf in #147
• Uncomment dim reduction tests by @lazigu in #150
• Change pypi badge to conda one by @lazigu in #152
• Fix a couple of small bugs by @lazigu in #155
• Update readme by @lazigu in #156

Full Changelog: 0.5.2...0.6.0

0.5.2

What's Changed

• update version by @haesleinhuepf in #111
• Create CITATION.cff by @lazigu in #121. It is now possible to cite the repository from the "about" section in the sidebar.
• Fixing scale inheritance by @Cryaaa in #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 #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 #127. Thanks to @jaimergp for spotting!

Full Changelog: 0.5.1...0.5.2