small-fish-gui 2.0.2__py3-none-any.whl → 2.0.3__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 (51) hide show
  1. small_fish_gui/__init__.py +2 -2
  2. small_fish_gui/batch/integrity.py +2 -2
  3. small_fish_gui/batch/pipeline.py +46 -11
  4. small_fish_gui/batch/prompt.py +102 -41
  5. small_fish_gui/batch/update.py +26 -13
  6. small_fish_gui/batch/utils.py +1 -1
  7. small_fish_gui/gui/__init__.py +1 -0
  8. small_fish_gui/gui/_napari_widgets.py +418 -6
  9. small_fish_gui/gui/layout.py +332 -112
  10. small_fish_gui/gui/napari_visualiser.py +107 -22
  11. small_fish_gui/gui/prompts.py +161 -48
  12. small_fish_gui/gui/testing.ipynb +231 -24
  13. small_fish_gui/gui/tooltips.py +7 -1
  14. small_fish_gui/hints.py +23 -7
  15. small_fish_gui/interface/__init__.py +7 -1
  16. small_fish_gui/interface/default_settings.py +118 -0
  17. small_fish_gui/interface/image.py +43 -11
  18. small_fish_gui/interface/settings.json +50 -0
  19. small_fish_gui/interface/testing.ipynb +4354 -0
  20. small_fish_gui/interface/user_settings.py +96 -0
  21. small_fish_gui/main_menu.py +13 -1
  22. small_fish_gui/pipeline/{_signaltonoise.py → _bigfish_wrapers.py} +59 -7
  23. small_fish_gui/pipeline/_colocalisation.py +23 -24
  24. small_fish_gui/pipeline/_preprocess.py +46 -32
  25. small_fish_gui/pipeline/actions.py +48 -5
  26. small_fish_gui/pipeline/detection.py +71 -141
  27. small_fish_gui/pipeline/segmentation.py +360 -268
  28. small_fish_gui/pipeline/spots.py +3 -3
  29. small_fish_gui/pipeline/utils.py +5 -1
  30. small_fish_gui/README.md → small_fish_gui-2.0.3.dist-info/METADATA +35 -0
  31. small_fish_gui-2.0.3.dist-info/RECORD +46 -0
  32. {small_fish_gui-2.0.2.dist-info → small_fish_gui-2.0.3.dist-info}/WHEEL +1 -1
  33. small_fish_gui/.github/workflows/python-publish.yml +0 -39
  34. small_fish_gui/LICENSE +0 -24
  35. small_fish_gui/batch/values.txt +0 -65
  36. small_fish_gui/default_values.py +0 -51
  37. small_fish_gui/gui/screenshot/general_help_screenshot.png +0 -0
  38. small_fish_gui/gui/screenshot/mapping_help_screenshot.png +0 -0
  39. small_fish_gui/gui/screenshot/segmentation_help_screenshot.png +0 -0
  40. small_fish_gui/illustrations/DetectionVitrine_filtre.png +0 -0
  41. small_fish_gui/illustrations/DetectionVitrine_signal.png +0 -0
  42. small_fish_gui/illustrations/FocciVitrine.png +0 -0
  43. small_fish_gui/illustrations/FocciVitrine_no_spots.png +0 -0
  44. small_fish_gui/illustrations/Segmentation2D.png +0 -0
  45. small_fish_gui/illustrations/Segmentation2D_with_labels.png +0 -0
  46. small_fish_gui/logo.png +0 -0
  47. small_fish_gui/pipeline/testing.ipynb +0 -3636
  48. small_fish_gui/requirements.txt +0 -19
  49. small_fish_gui-2.0.2.dist-info/METADATA +0 -75
  50. small_fish_gui-2.0.2.dist-info/RECORD +0 -59
  51. {small_fish_gui-2.0.2.dist-info → small_fish_gui-2.0.3.dist-info}/licenses/LICENSE +0 -0
small_fish_gui/requirements.txt DELETED
@@ -1,19 +0,0 @@
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- big-fish==0.6.2
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- cellpose>=4.0.6
3
- czifile>=2019.7.2
4
- imageio>=2.34.0
5
- napari>=0.4.19.post1
6
- napari-console>=0.0.9
7
- napari-plugin-engine>=0.2.0
8
- napari-plugin-manager>=0.1.0a2
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- napari-svg>=0.1.10
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- numpy>=1.24.4
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- pandas>=1.5.3
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- FreeSimpleGUI>=5.1.1
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- scipy>=1.9.1
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- scikit-image==0.19.1
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- 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
small_fish_gui-2.0.2.dist-info/METADATA DELETED
@@ -1,75 +0,0 @@
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- Metadata-Version: 2.4
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- Name: small_fish_gui
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- Version: 2.0.2
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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/SmallFishGUI/small_fish_gui
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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_gui/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
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- 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: big-fish==0.6.2
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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: 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: 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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- Description-Content-Type: text/markdown
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-
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- # Small Fish
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- **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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-
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- Cell segmentation is peformed using *cellpose* (published work) : https://github.com/MouseLand/cellpose
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-
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- Spot detection is performed via *big-fish* (published work) : https://github.com/fish-quant/big-fish
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-
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- Time stacks are not supported.
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-
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- ## Installation
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-
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- It is higly recommanded to create a specific [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) or [virtual](https://docs.python.org/3.6/library/venv.html) environnement to install small fish.
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-
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- ```bash
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- conda create -n small_fish python=3.8
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- activate small_fish
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- ```
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- Then download the small_fish package :
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- ```bash
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- pip install small_fish
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- ```
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- <b> (Recommended) </b> Results visualisation is achieved through *Napari* which you can install with :
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-
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- ```bash
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- pip install napari[all]
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- ```
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-
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- ## Run Small fish
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-
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- First activate your python environnement :
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- ```bash
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- activate small_fish
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- ```
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- Then launch Small fish :
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- ```bash
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- python -m small_fish
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- ```
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- ## Developpement
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-
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- Optional features to include in future versions :
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- - time stack (which would include cell tracking)
small_fish_gui-2.0.2.dist-info/RECORD DELETED
@@ -1,59 +0,0 @@
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- small_fish_gui/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
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- small_fish_gui/__init__.py,sha256=WNInvg3HaKrfuEOQHmnnZ5SoI-5o3EFgapeiX0rbzqo,2162
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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/utils.py,sha256=LM6QW2ono_LIRv7JXIIq7ZxxbDXqBtZ5uR9gjKJfwM8,1903
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