Aydin

What's Changed
* DEP: Pyinstaller bump to 5.1 by AhmetCanSolak in https://github.com/royerlab/aydin/pull/187
* GUI: main layout refactor by AhmetCanSolak in https://github.com/royerlab/aydin/pull/190
* BUG: GUI layout name bug by AhmetCanSolak in https://github.com/royerlab/aydin/pull/191
* CONTRIBUTING guidelines update by AhmetCanSolak in https://github.com/royerlab/aydin/pull/194
* IT-CNN default patch_size value by AhmetCanSolak in https://github.com/royerlab/aydin/pull/195
* CLI: Split channels by AhmetCanSolak in https://github.com/royerlab/aydin/pull/197
* Contributing guideline updates by AhmetCanSolak in https://github.com/royerlab/aydin/pull/199
* napari version bump to 0.4.15 by AhmetCanSolak in https://github.com/royerlab/aydin/pull/206
* DOC: it level docstrings refactor by AhmetCanSolak in https://github.com/royerlab/aydin/pull/201
* Restoration variant option bug fix and refactor by AhmetCanSolak in https://github.com/royerlab/aydin/pull/203
* Making dependency pinnings bundle only by AhmetCanSolak in https://github.com/royerlab/aydin/pull/202
* torch input and target images tiling by AhmetCanSolak in https://github.com/royerlab/aydin/pull/192
* build: osx hook fix by AhmetCanSolak in https://github.com/royerlab/aydin/pull/208
* Torch unet n2t training loop refactor by AhmetCanSolak in https://github.com/royerlab/aydin/pull/210
* Torch unet maskout by AhmetCanSolak in https://github.com/royerlab/aydin/pull/209
* BUG: GUI: denoise tab selection persistence by AhmetCanSolak in https://github.com/royerlab/aydin/pull/212
* pytest general test speed-up by AhmetCanSolak in https://github.com/royerlab/aydin/pull/211
* Torch unet fstring fixes by AhmetCanSolak in https://github.com/royerlab/aydin/pull/213
* Torch original unet by AhmetCanSolak in https://github.com/royerlab/aydin/pull/216
* Torch unet residual by AhmetCanSolak in https://github.com/royerlab/aydin/pull/215
* Torch model demos by AhmetCanSolak in https://github.com/royerlab/aydin/pull/218
* Torch Linear Scaling UNet by AhmetCanSolak in https://github.com/royerlab/aydin/pull/217
* Relaxing torch dependency version by AhmetCanSolak in https://github.com/royerlab/aydin/pull/219
* Relaxing gdown version by AhmetCanSolak in https://github.com/royerlab/aydin/pull/220
* Misc. test fixes by AhmetCanSolak in https://github.com/royerlab/aydin/pull/221
* Relaxing click dependency version by AhmetCanSolak in https://github.com/royerlab/aydin/pull/224
* Removing googledrivedownloader from dependencies by AhmetCanSolak in https://github.com/royerlab/aydin/pull/225
* Relaxing nd2reader pinning by AhmetCanSolak in https://github.com/royerlab/aydin/pull/226
* Relaxing memoization version by AhmetCanSolak in https://github.com/royerlab/aydin/pull/229
* Relaxing numexpr version by AhmetCanSolak in https://github.com/royerlab/aydin/pull/228
* Relaxing scipy version by AhmetCanSolak in https://github.com/royerlab/aydin/pull/227
* Removing unused code by AhmetCanSolak in https://github.com/royerlab/aydin/pull/230
* Catboost regressor refactor by AhmetCanSolak in https://github.com/royerlab/aydin/pull/222
* Relaxing pynndescent version by AhmetCanSolak in https://github.com/royerlab/aydin/pull/231
* CB regressor bug fix by AhmetCanSolak in https://github.com/royerlab/aydin/pull/232
* Fourier Shell Correlation by AhmetCanSolak in https://github.com/royerlab/aydin/pull/223
* fixed min max number of estimators by royerloic in https://github.com/royerlab/aydin/pull/234
* GUI: new egg chamber example dataset by AhmetCanSolak in https://github.com/royerlab/aydin/pull/237
* DOC: Example datasets gallery by AhmetCanSolak in https://github.com/royerlab/aydin/pull/236
* removing unused util misc modules by AhmetCanSolak in https://github.com/royerlab/aydin/pull/240
* New random patch generation function by AhmetCanSolak in https://github.com/royerlab/aydin/pull/239
* BUG: restoration cnn channel_axes parameter check fix by AhmetCanSolak in https://github.com/royerlab/aydin/pull/241
* Torch unet n2s by AhmetCanSolak in https://github.com/royerlab/aydin/pull/214
* torch random pixel masking by AhmetCanSolak in https://github.com/royerlab/aydin/pull/242
* zarr version is unpinned by AhmetCanSolak in https://github.com/royerlab/aydin/pull/243
* Torch jinet implementation by AhmetCanSolak in https://github.com/royerlab/aydin/pull/196
* CLI: fsc command by AhmetCanSolak in https://github.com/royerlab/aydin/pull/246
* Torch tests demos refactor by AhmetCanSolak in https://github.com/royerlab/aydin/pull/245
* BUG: 3D jinet bug patch by AhmetCanSolak in https://github.com/royerlab/aydin/pull/244
* psnr ssim print statements for demos and tests by AhmetCanSolak in https://github.com/royerlab/aydin/pull/247
* Deprecate Tensorflow related code by AhmetCanSolak in https://github.com/royerlab/aydin/pull/249
* Py310 support by AhmetCanSolak in https://github.com/royerlab/aydin/pull/248
* imagio version fix by AhmetCanSolak in https://github.com/royerlab/aydin/pull/253
* numexpr to numba by AhmetCanSolak in https://github.com/royerlab/aydin/pull/252
* Versioning for docs by AhmetCanSolak in https://github.com/royerlab/aydin/pull/254
* sphinx-multiversion dependency added by AhmetCanSolak in https://github.com/royerlab/aydin/pull/256
* Torch it cnn by AhmetCanSolak in https://github.com/royerlab/aydin/pull/250
* fix on n2t tests by AhmetCanSolak in https://github.com/royerlab/aydin/pull/258
* github labeler by AhmetCanSolak in https://github.com/royerlab/aydin/pull/257
* BUG: fix for cnn restoration by AhmetCanSolak in https://github.com/royerlab/aydin/pull/260
* Heavy tests action by AhmetCanSolak in https://github.com/royerlab/aydin/pull/261
* Removing numba deprecation warnings by AhmetCanSolak in https://github.com/royerlab/aydin/pull/262


**Full Changelog**: https://github.com/royerlab/aydin/compare/v0.1.14...v0.1.15

What's Changed
* bundle urls updated upon new release by AhmetCanSolak in https://github.com/royerlab/aydin/pull/157
* Current fixes by royerloic in https://github.com/royerlab/aydin/pull/158
* DOC: OpenCell Use Case by AhmetCanSolak in https://github.com/royerlab/aydin/pull/159
* Update README.md by AhmetCanSolak in https://github.com/royerlab/aydin/pull/160
* DOC: build warnings resolutions by AhmetCanSolak in https://github.com/royerlab/aydin/pull/162
* DOC: removing why_aydin.rst from build checks by AhmetCanSolak in https://github.com/royerlab/aydin/pull/164
* Restoration: Unused code refactor by AhmetCanSolak in https://github.com/royerlab/aydin/pull/165
* CLI: lucyrichardson refactor by AhmetCanSolak in https://github.com/royerlab/aydin/pull/166
* CLI: Click tests for CLI commands by AhmetCanSolak in https://github.com/royerlab/aydin/pull/132
* DOC: Classic denoisers API reference by AhmetCanSolak in https://github.com/royerlab/aydin/pull/168
* GUI: Removing pyqt5 imports by AhmetCanSolak in https://github.com/royerlab/aydin/pull/169
* GUI: Super class call bug fix by AhmetCanSolak in https://github.com/royerlab/aydin/pull/170
* GUI: range label for cropping sliders by AhmetCanSolak in https://github.com/royerlab/aydin/pull/171
* DEP: numexpr version to 2.8.1 by AhmetCanSolak in https://github.com/royerlab/aydin/pull/175
* CLI: psnr command typo fixes by AhmetCanSolak in https://github.com/royerlab/aydin/pull/177
* CLI: mse command by AhmetCanSolak in https://github.com/royerlab/aydin/pull/178
* CLI: test bug fix by AhmetCanSolak in https://github.com/royerlab/aydin/pull/179
* DEP: Tensorflow version to 2.8.1, Keras to 2.8.0 by AhmetCanSolak in https://github.com/royerlab/aydin/pull/174
* IO: Tests cannot find hela dataset by AhmetCanSolak in https://github.com/royerlab/aydin/pull/180
* DOC: Use case updates by AhmetCanSolak in https://github.com/royerlab/aydin/pull/182
* DOC: changing use case order by AhmetCanSolak in https://github.com/royerlab/aydin/pull/183
* Latest fixes by royerloic in https://github.com/royerlab/aydin/pull/181
* DOC: follow-up after use case updates by AhmetCanSolak in https://github.com/royerlab/aydin/pull/184
* CI: protobuf install fix by AhmetCanSolak in https://github.com/royerlab/aydin/pull/185
* DEP: numba to 0.55.1 by AhmetCanSolak in https://github.com/royerlab/aydin/pull/176
* BUILD: Adding missing hiddenimports by AhmetCanSolak in https://github.com/royerlab/aydin/pull/186
* BUG: Latest protobuf import error resolution by AhmetCanSolak in https://github.com/royerlab/aydin/pull/188
* DOC: Chicken embryo use case by AhmetCanSolak in https://github.com/royerlab/aydin/pull/189


**Full Changelog**: https://github.com/royerlab/aydin/compare/v0.1.13...v0.1.14

What's Changed
* pyinstaller version upgraded by AhmetCanSolak in https://github.com/royerlab/aydin/pull/89
* Bundle links updated after new release by AhmetCanSolak in https://github.com/royerlab/aydin/pull/90
* GUI: editable output paths by AhmetCanSolak in https://github.com/royerlab/aydin/pull/84
* BUG: cli lucyrichardson psf reading bug fix by AhmetCanSolak in https://github.com/royerlab/aydin/pull/92
* GUI: Removing train_on field from data model by AhmetCanSolak in https://github.com/royerlab/aydin/pull/93
* DOC: gui output folder tutorial by AhmetCanSolak in https://github.com/royerlab/aydin/pull/94
* Update LICENSE.txt by AhmetCanSolak in https://github.com/royerlab/aydin/pull/96
* DOC: sphinx-copybuton by AhmetCanSolak in https://github.com/royerlab/aydin/pull/98
* UNet model in pytorch by AhmetCanSolak in https://github.com/royerlab/aydin/pull/79
* Scipy version fix by AhmetCanSolak in https://github.com/royerlab/aydin/pull/100
* Temporary nn structure by AhmetCanSolak in https://github.com/royerlab/aydin/pull/101
* GUI: Load pretrained models by AhmetCanSolak in https://github.com/royerlab/aydin/pull/97
* Restoration module level load model by AhmetCanSolak in https://github.com/royerlab/aydin/pull/103
* TEST: adding saveload tests on restoration level by AhmetCanSolak in https://github.com/royerlab/aydin/pull/104
* BUG: GUI pretrained model usage by AhmetCanSolak in https://github.com/royerlab/aydin/pull/102
* Removing default txt by AhmetCanSolak in https://github.com/royerlab/aydin/pull/107
* GUI: Removing code duplication on denoise tab refreshes by AhmetCanSolak in https://github.com/royerlab/aydin/pull/108
* Pypi download badge by AhmetCanSolak in https://github.com/royerlab/aydin/pull/109
* LGBM save model fix by AhmetCanSolak in https://github.com/royerlab/aydin/pull/111
* Improvements to aydin docstrings by royerloic in https://github.com/royerlab/aydin/pull/110
* numpy sqrt refactor by AhmetCanSolak in https://github.com/royerlab/aydin/pull/112
* DOC: Perceptron regressor updates by AhmetCanSolak in https://github.com/royerlab/aydin/pull/113
* Improve classic optimiser by royerloic in https://github.com/royerlab/aydin/pull/114
* Github actions to do style and lint checks by AhmetCanSolak in https://github.com/royerlab/aydin/pull/117
* Flake fixes by AhmetCanSolak in https://github.com/royerlab/aydin/pull/120
* Github actions test task by AhmetCanSolak in https://github.com/royerlab/aydin/pull/119
* Bug fix on classic restoration implementation by AhmetCanSolak in https://github.com/royerlab/aydin/pull/121
* Dim analysis by royerloic in https://github.com/royerlab/aydin/pull/118
* GUI: text wrapping fixes by AhmetCanSolak in https://github.com/royerlab/aydin/pull/95
* FGR blind_spots argumet duplication fix by AhmetCanSolak in https://github.com/royerlab/aydin/pull/123
* Fixing bugs by royerloic in https://github.com/royerlab/aydin/pull/124
* CI: Test task dependency fix by AhmetCanSolak in https://github.com/royerlab/aydin/pull/125
* GUI: Cropping tabs Z step update by AhmetCanSolak in https://github.com/royerlab/aydin/pull/127
* CI: capturing only related output by AhmetCanSolak in https://github.com/royerlab/aydin/pull/128
* GUI: Text wrapping for parameter names by AhmetCanSolak in https://github.com/royerlab/aydin/pull/130
* CatBoost Regressor learning_rate seed by AhmetCanSolak in https://github.com/royerlab/aydin/pull/129
* More improvements by royerloic in https://github.com/royerlab/aydin/pull/126
* Classic denoisers interpolation mode default value by AhmetCanSolak in https://github.com/royerlab/aydin/pull/134
* Refactor: namedtuple defaults for classic denoisers by AhmetCanSolak in https://github.com/royerlab/aydin/pull/135
* GUI: Disabling spatial features by AhmetCanSolak in https://github.com/royerlab/aydin/pull/136
* GUI: Auto crop for training data Z and T dimensions by AhmetCanSolak in https://github.com/royerlab/aydin/pull/139
* GUI: Spatial feature disabling bug fix by AhmetCanSolak in https://github.com/royerlab/aydin/pull/140
* Classic restoration ImageTranslator level args by AhmetCanSolak in https://github.com/royerlab/aydin/pull/142
* Catboost version bump to 1.0.5 by AhmetCanSolak in https://github.com/royerlab/aydin/pull/141
* CLI: psnr and ssim commands by AhmetCanSolak in https://github.com/royerlab/aydin/pull/145
* Minor fixes -- actually not so minor... by royerloic in https://github.com/royerlab/aydin/pull/144
* BUG: Dimension Analysis by AhmetCanSolak in https://github.com/royerlab/aydin/pull/147
* Update CONTRIBUTING.md by AhmetCanSolak in https://github.com/royerlab/aydin/pull/149
* BUG: CLI hyperstack command file output by AhmetCanSolak in https://github.com/royerlab/aydin/pull/150
* Final fixes before new release by royerloic in https://github.com/royerlab/aydin/pull/148
* DEP: distributed by AhmetCanSolak in https://github.com/royerlab/aydin/pull/153
* Even faster cropping by royerloic in https://github.com/royerlab/aydin/pull/152
* BUG: super fast crop zoom call fix by AhmetCanSolak in https://github.com/royerlab/aydin/pull/154
* BUG: Build scipy missing hooks by AhmetCanSolak in https://github.com/royerlab/aydin/pull/155


**Full Changelog**: https://github.com/royerlab/aydin/compare/v0.1.12...v0.1.13

What's Changed
* updating bundle links by AhmetCanSolak in https://github.com/royerlab/aydin/pull/57
* adding options json page on docs by AhmetCanSolak in https://github.com/royerlab/aydin/pull/60
* CLI: enabling batch axes and channel axes arguments on CLI by AhmetCanSolak in https://github.com/royerlab/aydin/pull/62
* GUI: handling mistyped parameters by AhmetCanSolak in https://github.com/royerlab/aydin/pull/65
* DOC: cli tutorial on how to pass batch dimensions by AhmetCanSolak in https://github.com/royerlab/aydin/pull/66
* GUI: separating npr viewer and model definitions by AhmetCanSolak in https://github.com/royerlab/aydin/pull/67
* BUILD: linux fixes by AhmetCanSolak in https://github.com/royerlab/aydin/pull/68
* BUILD: osx build fixes after required package updates by AhmetCanSolak in https://github.com/royerlab/aydin/pull/69
* BUILD: Bug fix after scikit-learn version upgrade by AhmetCanSolak in https://github.com/royerlab/aydin/pull/71
* BUILD: Windows fixes related to imageio and numba by AhmetCanSolak in https://github.com/royerlab/aydin/pull/72
* importlib-metadata version upgraded by AhmetCanSolak in https://github.com/royerlab/aydin/pull/73
* Refactor: bringing back ArrayLike type annotations to it.transforms by AhmetCanSolak in https://github.com/royerlab/aydin/pull/75
* GUI: Basic/Advanced modes toggle feature by AhmetCanSolak in https://github.com/royerlab/aydin/pull/64
* GUI: Hiding advanced processing tabs when basic mode is active by AhmetCanSolak in https://github.com/royerlab/aydin/pull/76
* Refactor: Misc gui code refactor by AhmetCanSolak in https://github.com/royerlab/aydin/pull/77
* Refactor: It cnn file refactor by AhmetCanSolak in https://github.com/royerlab/aydin/pull/78
* GUI: Saving processing related details by AhmetCanSolak in https://github.com/royerlab/aydin/pull/80
* BUG: Aydin CLI was not saving model by AhmetCanSolak in https://github.com/royerlab/aydin/pull/81
* DOC: Contributing guideline update by AhmetCanSolak in https://github.com/royerlab/aydin/pull/83
* BUG: CLI was crashing with multiple images by AhmetCanSolak in https://github.com/royerlab/aydin/pull/86
* CLI: output folder option by AhmetCanSolak in https://github.com/royerlab/aydin/pull/85
* DOC: CLI tutorial on output folder arg by AhmetCanSolak in https://github.com/royerlab/aydin/pull/87
* BUG: Fixing after breaking regressor name refactor by AhmetCanSolak in https://github.com/royerlab/aydin/pull/88


**Full Changelog**: https://github.com/royerlab/aydin/compare/v0.1.11...v0.1.12

What's Changed
* version update to v0.1.9 by AhmetCanSolak in https://github.com/royerlab/aydin/pull/38
* doi-addition-to-docs by AhmetCanSolak in https://github.com/royerlab/aydin/pull/39
* Update issue templates by AhmetCanSolak in https://github.com/royerlab/aydin/pull/41
* cli tutorial fixes by AhmetCanSolak in https://github.com/royerlab/aydin/pull/45
* Docs fixes demo fixes numba features fix by AhmetCanSolak in https://github.com/royerlab/aydin/pull/46
* update on README.md by AhmetCanSolak in https://github.com/royerlab/aydin/pull/47
* Update README.md by Abdur-rahmaanJ in https://github.com/royerlab/aydin/pull/42
* DOC: install add libomp warning added to install page by AhmetCanSolak in https://github.com/royerlab/aydin/pull/48
* Adding image.sc links by AhmetCanSolak in https://github.com/royerlab/aydin/pull/49
* adding doi to cli and gui by AhmetCanSolak in https://github.com/royerlab/aydin/pull/50
* adding links across docs gui and repository by AhmetCanSolak in https://github.com/royerlab/aydin/pull/51
* dependency version updates by AhmetCanSolak in https://github.com/royerlab/aydin/pull/52
* docs api tutorials import fixes on restoration modules by AhmetCanSolak in https://github.com/royerlab/aydin/pull/54
* adding py39 disclaimer to getting started section in docs by AhmetCanSolak in https://github.com/royerlab/aydin/pull/55
* osx build splash screen fix by AhmetCanSolak in https://github.com/royerlab/aydin/pull/56

New Contributors
* Abdur-rahmaanJ made their first contribution in https://github.com/royerlab/aydin/pull/42

**Full Changelog**: https://github.com/royerlab/aydin/compare/v0.1.9...v0.1.11

What's Changed
* docs-adding-bundle-links by AhmetCanSolak in https://github.com/royerlab/aydin/pull/32
* gui-example-datasets-renaming by AhmetCanSolak in https://github.com/royerlab/aydin/pull/33
* adding-precommit-config by AhmetCanSolak in https://github.com/royerlab/aydin/pull/34
* docs-connecting-missing-links by AhmetCanSolak in https://github.com/royerlab/aydin/pull/35
* Hyers by AhmetCanSolak in https://github.com/royerlab/aydin/pull/36
* docs-making-github-issue-link-work by AhmetCanSolak in https://github.com/royerlab/aydin/pull/37


**Full Changelog**: https://github.com/royerlab/aydin/compare/v0.1.8...v0.1.9