small-fish-gui 2.0.2__py3-none-any.whl → 2.1.0__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-2.1.0.dist-info/METADATA +48 -8
  31. small_fish_gui-2.1.0.dist-info/RECORD +46 -0
  32. {small_fish_gui-2.0.2.dist-info → small_fish_gui-2.1.0.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-2.1.0.dist-info}/licenses/LICENSE +0 -0
small_fish_gui/interface/settings.json ADDED
@@ -0,0 +1,50 @@
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+ {
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+ "working_directory": "/media/SSD_floricslimani",
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+ "do_background_removal": false,
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+ "background_channel": 0,
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+ "multichannel_stack": true,
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+ "stack_3D": true,
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+ "detection_channel": 0,
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+ "nucleus_channel": 1,
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+ "anisotropy": 1.0,
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+ "flow_threshold": 0.4,
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+ "cellprob_threshold": 0.0,
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+ "cytoplasm_diameter": 90,
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+ "cytoplasm_min_size": 15,
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+ "cytoplasm_max_proj": false,
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+ "cytoplasm_mean_proj": true,
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+ "cytoplasm_select_slice": false,
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+ "cytoplasm_selected_slice": 0,
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+ "nucleus_diameter": 60,
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+ "cytoplasm_model": "cpsam",
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+ "nucleus_model": "cpsam",
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+ "nucleus_min_size": 15,
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+ "nucleus_max_proj": false,
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+ "nucleus_mean_proj": true,
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+ "nucleus_select_slice": false,
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+ "nucleus_selected_slice": 0,
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+ "show_segmentation": true,
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+ "segment_only_nuclei": false,
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+ "do_3D_segmentation": false,
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+ "save_segmentation_visuals": false,
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+ "threshold": null,
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+ "threshold_penalty": 1.0,
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+ "do_dense_regions_deconvolution": false,
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+ "do_cluster": false,
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+ "show_napari_corrector": true,
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+ "interactive_threshold_selector": false,
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+ "alpha": 0.5,
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+ "beta": 1.0,
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+ "gamma": 3.0,
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+ "cluster_size": 400,
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+ "min_spot": 5,
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+ "coloc_range": 400,
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+ "do_csv": false,
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+ "do_excel": false,
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+ "spot_extraction_folder": "/home/floric",
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+ "voxel_size": [
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+ 1,
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+ 2,
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+ 3
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+ ]
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+ }