small-fish-gui 1.10.4__py3-none-any.whl → 2.0.1__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (39) hide show
  1. small_fish_gui/README.md +42 -70
  2. small_fish_gui/__init__.py +1 -1
  3. small_fish_gui/__main__.py +1 -1
  4. small_fish_gui/batch/integrity.py +8 -1
  5. small_fish_gui/batch/output.py +16 -0
  6. small_fish_gui/batch/pipeline.py +43 -24
  7. small_fish_gui/batch/prompt.py +44 -26
  8. small_fish_gui/batch/update.py +19 -3
  9. small_fish_gui/batch/utils.py +2 -0
  10. small_fish_gui/batch/values.txt +5 -5
  11. small_fish_gui/default_values.py +51 -0
  12. small_fish_gui/gui/__init__.py +3 -1
  13. small_fish_gui/gui/_napari_widgets.py +15 -4
  14. small_fish_gui/gui/layout.py +123 -54
  15. small_fish_gui/gui/napari_visualiser.py +12 -8
  16. small_fish_gui/gui/prompts.py +61 -74
  17. small_fish_gui/gui/tooltips.py +15 -0
  18. small_fish_gui/hints.py +23 -4
  19. small_fish_gui/illustrations/DetectionVitrine_filtre.png +0 -0
  20. small_fish_gui/illustrations/DetectionVitrine_signal.png +0 -0
  21. small_fish_gui/illustrations/FocciVitrine.png +0 -0
  22. small_fish_gui/illustrations/FocciVitrine_no_spots.png +0 -0
  23. small_fish_gui/illustrations/Segmentation2D.png +0 -0
  24. small_fish_gui/illustrations/Segmentation2D_with_labels.png +0 -0
  25. small_fish_gui/logo.png +0 -0
  26. small_fish_gui/{pipeline/main.py → main_menu.py} +16 -15
  27. small_fish_gui/pipeline/_colocalisation.py +60 -41
  28. small_fish_gui/pipeline/_preprocess.py +13 -12
  29. small_fish_gui/pipeline/actions.py +102 -14
  30. small_fish_gui/pipeline/detection.py +5 -1
  31. small_fish_gui/pipeline/segmentation.py +206 -73
  32. small_fish_gui/pipeline/spots.py +129 -5
  33. small_fish_gui/pipeline/testing.ipynb +1571 -2
  34. small_fish_gui/requirements.txt +4 -4
  35. {small_fish_gui-1.10.4.dist-info → small_fish_gui-2.0.1.dist-info}/METADATA +14 -16
  36. small_fish_gui-2.0.1.dist-info/RECORD +59 -0
  37. small_fish_gui-1.10.4.dist-info/RECORD +0 -49
  38. {small_fish_gui-1.10.4.dist-info → small_fish_gui-2.0.1.dist-info}/WHEEL +0 -0
  39. {small_fish_gui-1.10.4.dist-info → small_fish_gui-2.0.1.dist-info}/licenses/LICENSE +0 -0
small_fish_gui/requirements.txt CHANGED
@@ -1,7 +1,7 @@
1
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  big-fish==0.6.2
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- cellpose==3.0.7
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- czifile==2019.7.2
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- imageio==2.34.0
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+ cellpose>=4.0.6
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+ czifile>=2019.7.2
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+ imageio>=2.34.0
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  napari>=0.4.19.post1
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  napari-console>=0.0.9
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  napari-plugin-engine>=0.2.0
@@ -16,4 +16,4 @@ scikit-learn==1.3.2
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  openpyxl>=3.1.2
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  pyarrow>=11.0.0
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  aicsimageio>=aicsimageio==4.14.0
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- aicspylibczi==3.3.1
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+ aicspylibczi>=3.3.1
{small_fish_gui-1.10.4.dist-info → small_fish_gui-2.0.1.dist-info}/METADATA RENAMED
@@ -1,10 +1,10 @@
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  Metadata-Version: 2.4
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  Name: small_fish_gui
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- Version: 1.10.4
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+ Version: 2.0.1
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  Summary: Small Fish is a python application for the analysis of smFish images. It provides a ready to use graphical interface to combine famous python packages for cell analysis without any need for coding.
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- Project-URL: Homepage, https://github.com/2Echoes/small_fish
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- Project-URL: Wiki, https://github.com/2Echoes/small_fish_gui/wiki
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- Project-URL: Issues, https://github.com/2Echoes/small_fish/issues
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+ Project-URL: Homepage, https://github.com/SmallFishGUI/small_fish
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+ Project-URL: Wiki, https://github.com/SmallFishGUI/small_fish_gui/wiki
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+ Project-URL: Issues, https://github.com/SmallFishGUI/small_fish/issues
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  Author-email: Slimani Floric <floric.slimani@live.com>
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  License-File: LICENSE
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  Classifier: License :: OSI Approved :: BSD License
@@ -12,24 +12,24 @@ Classifier: Operating System :: OS Independent
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  Classifier: Programming Language :: Python :: 3
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  Requires-Python: >=3.9
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  Requires-Dist: aicsimageio>=4.14.0
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- Requires-Dist: aicspylibczi==3.3.1
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+ Requires-Dist: aicspylibczi>=3.3.1
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  Requires-Dist: big-fish==0.6.2
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- Requires-Dist: cellpose==3.0.7
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- Requires-Dist: czifile==2019.7.2
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+ Requires-Dist: cellpose>=4.0.6
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+ Requires-Dist: czifile>=2019.7.2
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  Requires-Dist: freesimplegui>=5.1.1
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- Requires-Dist: imageio==2.34.0
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+ Requires-Dist: imageio>=2.34.0
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  Requires-Dist: napari-console>=0.0.9
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  Requires-Dist: napari-plugin-engine>=0.2.0
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  Requires-Dist: napari-plugin-manager>=0.1.0a2
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  Requires-Dist: napari-svg>=0.1.10
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  Requires-Dist: napari>=0.4.19.post1
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  Requires-Dist: numpy>=1.24.4
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- Requires-Dist: openpyxl==3.1.2
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+ Requires-Dist: openpyxl>=3.1.2
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  Requires-Dist: pandas>=1.5.3
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- Requires-Dist: pyarrow==11.0.0
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- Requires-Dist: scikit-image==0.19.1
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- Requires-Dist: scikit-learn==1.3.2
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- Requires-Dist: scipy>=1.9.1
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+ Requires-Dist: pyarrow>=11.0.0
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+ Requires-Dist: scikit-image>=0.19.1
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+ Requires-Dist: scikit-learn>=1.3.2
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+ Requires-Dist: scipy==1.9.1
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  Description-Content-Type: text/markdown
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  # Small Fish
@@ -39,7 +39,7 @@ Cell segmentation is peformed using *cellpose* (published work) : https://github
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  Spot detection is performed via *big-fish* (published work) : https://github.com/fish-quant/big-fish
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- Time stacks are not yet supported.
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+ Time stacks are not supported.
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  ## Installation
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@@ -72,6 +72,4 @@ python -m small_fish
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  ## Developpement
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  Optional features to include in future versions :
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- - batch processing
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  - time stack (which would include cell tracking)
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- - 3D segmentation
small_fish_gui-2.0.1.dist-info/RECORD ADDED
@@ -0,0 +1,59 @@
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+ small_fish_gui/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
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+ small_fish_gui/README.md,sha256=L_cbKyeAcWpMNqUe1fbMi0I0CqXbdN7kvPlCrLnOCF4,3736
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+ small_fish_gui/__init__.py,sha256=zd6tWcL3jZ69_S-j99FJggZqvQhB7yYUrWq0So8z3-c,2049
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+ small_fish_gui/__main__.py,sha256=xwpFMDuo0kkYvPamyhlTHJ68bymDfbRpPzKy3SKwezY,1639
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+ small_fish_gui/default_values.py,sha256=E5eoCIyIgaA18WcD5EAUrbKoEXoEEEk6ml3JPvFd_GI,921
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+ small_fish_gui/hints.py,sha256=q8G9ZbV-y7EUyOa8MjCTJltu750EvhGCalAU8INzeoo,2703
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+ small_fish_gui/logo.png,sha256=giOvQ1OMAzQuTlH3zj8AdJWDr1lK0RHNnsdp5XFa3UY,306502
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+ small_fish_gui/main_menu.py,sha256=fLpC4NkP0hmeostXpgJWzu0De4ts02ne9l0WworlUEA,5842
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+ small_fish_gui/requirements.txt,sha256=i_WqyowfTBPDIcw5v9GFZzc5CGoO_UOHSoxV7D_ez3A,374
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+ small_fish_gui/utils.py,sha256=LM6QW2ono_LIRv7JXIIq7ZxxbDXqBtZ5uR9gjKJfwM8,1903
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+ small_fish_gui/.github/workflows/python-publish.yml,sha256=5Ltnuhw9TevhzndlBmdUgYMnS73xEAxSyd1u8DHdn5s,1084
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+ small_fish_gui/batch/__init__.py,sha256=ku2_Yate-UG89Q0BmE2B9kFV4kOz-u9Lf2lj6VsdFXs,127
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+ small_fish_gui/batch/input.py,sha256=mqnP8LBhyNbtlcqjVlUiVeuHw4YxOX3GgzJbq03isKE,1477
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+ small_fish_gui/batch/output.py,sha256=cKZBsO48HaKfxfa6cwcBKw3YRILBCcdC8rpYd2OTEVs,520
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+ small_fish_gui/batch/test.py,sha256=FcoCngSeueociwVoG8V3C6lQO7rrRHUfIVA2hJKr4v4,213
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+ small_fish_gui/batch/update.py,sha256=sA1ZOhKqDjvJUXa5uYe8WGcbAlJZYoRQD9w6hatfAZ8,5594
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+ small_fish_gui/batch/utils.py,sha256=edj_SwqBzSPb0jlV_LvO73ol0lT51fOiuV53dfNq1aY,1867
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+ small_fish_gui/gui/__init__.py,sha256=xt55Yl5zISMH9ifjlm-QDZCcQtpdaBJA12wiUJqM0B4,879
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+ small_fish_gui/gui/animation.py,sha256=MnYsA1kxQZ72L_H0knxOs41lG0ZZv1re7gSgYNmZY00,983
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+ small_fish_gui/gui/theme.py,sha256=30nujS48ZRdD1HVbzdEBkiAWlhow1AGgXSQNZcGEsaQ,118
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+ small_fish_gui/illustrations/DetectionVitrine_filtre.png,sha256=WE7J2ZcCqfahmqOtak31uts-xZc5gWJrodYChdyKX9U,203070
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+ small_fish_gui/illustrations/DetectionVitrine_signal.png,sha256=RA2l_RM77t1mWeCGHEXHVXuIGmBMyOC8iIUuGswnld0,374194
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+ small_fish_gui/illustrations/FocciVitrine.png,sha256=kB8gBGj4fjdk_sFD1hCjoiZhv2b7HjFpFoXLwwG5TeA,748087
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+ small_fish_gui/illustrations/FocciVitrine_no_spots.png,sha256=cEmN_Was9HABjvUZvQKAzC-1czNeGEVRdcWU3uWvjj8,712549
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+ small_fish_gui/illustrations/Segmentation2D.png,sha256=R4dHURvE39dvcj1ILCayRFNLxvUyeeIsMoheoEOa3rE,1577319
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+ small_fish_gui-2.0.1.dist-info/RECORD,,
small_fish_gui-1.10.4.dist-info/RECORD DELETED
@@ -1,49 +0,0 @@
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