celldetective 1.2.2__tar.gz → 1.2.2.post1__tar.gz

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 (98) hide show
  1. {celldetective-1.2.2 → celldetective-1.2.2.post1}/PKG-INFO +1 -1
  2. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective.egg-info/PKG-INFO +1 -1
  3. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective.egg-info/SOURCES.txt +0 -6
  4. {celldetective-1.2.2 → celldetective-1.2.2.post1}/setup.py +1 -1
  5. celldetective-1.2.2/celldetective/models/segmentation_effectors/primNK_cfse/config_input.json +0 -29
  6. celldetective-1.2.2/celldetective/models/segmentation_effectors/primNK_cfse/cp-cfse-transfer +0 -0
  7. celldetective-1.2.2/celldetective/models/segmentation_effectors/primNK_cfse/training_instructions.json +0 -37
  8. celldetective-1.2.2/celldetective/models/segmentation_effectors/ricm-bimodal/config_input.json +0 -130
  9. celldetective-1.2.2/celldetective/models/segmentation_effectors/ricm-bimodal/ricm-bimodal +0 -0
  10. celldetective-1.2.2/celldetective/models/segmentation_effectors/ricm-bimodal/training_instructions.json +0 -37
  11. {celldetective-1.2.2 → celldetective-1.2.2.post1}/LICENSE +0 -0
  12. {celldetective-1.2.2 → celldetective-1.2.2.post1}/README.md +0 -0
  13. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/__init__.py +0 -0
  14. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/__main__.py +0 -0
  15. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/datasets/segmentation_annotations/blank +0 -0
  16. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/datasets/signal_annotations/blank +0 -0
  17. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/events.py +0 -0
  18. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/extra_properties.py +0 -0
  19. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/filters.py +0 -0
  20. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/__init__.py +0 -0
  21. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/about.py +0 -0
  22. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/analyze_block.py +0 -0
  23. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/btrack_options.py +0 -0
  24. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/classifier_widget.py +0 -0
  25. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/configure_new_exp.py +0 -0
  26. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/control_panel.py +0 -0
  27. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/generic_signal_plot.py +0 -0
  28. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/gui_utils.py +0 -0
  29. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/json_readers.py +0 -0
  30. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/layouts.py +0 -0
  31. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/measurement_options.py +0 -0
  32. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/neighborhood_options.py +0 -0
  33. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/plot_measurements.py +0 -0
  34. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/plot_signals_ui.py +0 -0
  35. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/process_block.py +0 -0
  36. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/retrain_segmentation_model_options.py +0 -0
  37. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/retrain_signal_model_options.py +0 -0
  38. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/seg_model_loader.py +0 -0
  39. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/signal_annotator.py +0 -0
  40. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/signal_annotator2.py +0 -0
  41. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/signal_annotator_options.py +0 -0
  42. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/styles.py +0 -0
  43. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/survival_ui.py +0 -0
  44. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/tableUI.py +0 -0
  45. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/thresholds_gui.py +0 -0
  46. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/gui/viewers.py +0 -0
  47. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/icons/logo-large.png +0 -0
  48. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/icons/logo.png +0 -0
  49. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/icons/signals_icon.png +0 -0
  50. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/icons/splash-test.png +0 -0
  51. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/icons/splash.png +0 -0
  52. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/icons/splash0.png +0 -0
  53. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/icons/survival2.png +0 -0
  54. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/icons/vignette_signals2.png +0 -0
  55. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/icons/vignette_signals2.svg +0 -0
  56. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/io.py +0 -0
  57. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/links/zenodo.json +0 -0
  58. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/measure.py +0 -0
  59. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/models/pair_signal_detection/blank +0 -0
  60. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/models/segmentation_effectors/blank +0 -0
  61. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/models/segmentation_generic/blank +0 -0
  62. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/models/segmentation_targets/blank +0 -0
  63. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/models/signal_detection/blank +0 -0
  64. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/models/tracking_configs/mcf7.json +0 -0
  65. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/models/tracking_configs/ricm.json +0 -0
  66. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/models/tracking_configs/ricm2.json +0 -0
  67. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/neighborhood.py +0 -0
  68. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/preprocessing.py +0 -0
  69. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/relative_measurements.py +0 -0
  70. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/scripts/analyze_signals.py +0 -0
  71. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/scripts/measure_cells.py +0 -0
  72. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/scripts/measure_relative.py +0 -0
  73. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/scripts/segment_cells.py +0 -0
  74. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/scripts/segment_cells_thresholds.py +0 -0
  75. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/scripts/track_cells.py +0 -0
  76. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/scripts/train_segmentation_model.py +0 -0
  77. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/scripts/train_signal_model.py +0 -0
  78. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/segmentation.py +0 -0
  79. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/signals.py +0 -0
  80. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/tracking.py +0 -0
  81. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective/utils.py +0 -0
  82. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective.egg-info/dependency_links.txt +0 -0
  83. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective.egg-info/entry_points.txt +0 -0
  84. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective.egg-info/not-zip-safe +0 -0
  85. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective.egg-info/requires.txt +0 -0
  86. {celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective.egg-info/top_level.txt +0 -0
  87. {celldetective-1.2.2 → celldetective-1.2.2.post1}/setup.cfg +0 -0
  88. {celldetective-1.2.2 → celldetective-1.2.2.post1}/tests/__init__.py +0 -0
  89. {celldetective-1.2.2 → celldetective-1.2.2.post1}/tests/test_events.py +0 -0
  90. {celldetective-1.2.2 → celldetective-1.2.2.post1}/tests/test_filters.py +0 -0
  91. {celldetective-1.2.2 → celldetective-1.2.2.post1}/tests/test_io.py +0 -0
  92. {celldetective-1.2.2 → celldetective-1.2.2.post1}/tests/test_measure.py +0 -0
  93. {celldetective-1.2.2 → celldetective-1.2.2.post1}/tests/test_neighborhood.py +0 -0
  94. {celldetective-1.2.2 → celldetective-1.2.2.post1}/tests/test_preprocessing.py +0 -0
  95. {celldetective-1.2.2 → celldetective-1.2.2.post1}/tests/test_segmentation.py +0 -0
  96. {celldetective-1.2.2 → celldetective-1.2.2.post1}/tests/test_signals.py +0 -0
  97. {celldetective-1.2.2 → celldetective-1.2.2.post1}/tests/test_tracking.py +0 -0
  98. {celldetective-1.2.2 → celldetective-1.2.2.post1}/tests/test_utils.py +0 -0
{celldetective-1.2.2 → celldetective-1.2.2.post1}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: celldetective
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- Version: 1.2.2
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+ Version: 1.2.2.post1
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  Summary: description
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  Home-page: http://github.com/remyeltorro/celldetective
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  Author: Rémy Torro
{celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: celldetective
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- Version: 1.2.2
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+ Version: 1.2.2.post1
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  Summary: description
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  Home-page: http://github.com/remyeltorro/celldetective
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  Author: Rémy Torro
{celldetective-1.2.2 → celldetective-1.2.2.post1}/celldetective.egg-info/SOURCES.txt RENAMED
@@ -63,12 +63,6 @@ celldetective/icons/vignette_signals2.svg
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  celldetective/links/zenodo.json
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  celldetective/models/pair_signal_detection/blank
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  celldetective/models/segmentation_effectors/blank
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- celldetective/models/segmentation_effectors/primNK_cfse/config_input.json
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- celldetective/models/segmentation_effectors/primNK_cfse/cp-cfse-transfer
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- celldetective/models/segmentation_effectors/primNK_cfse/training_instructions.json
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- celldetective/models/segmentation_effectors/ricm-bimodal/config_input.json
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- celldetective/models/segmentation_effectors/ricm-bimodal/ricm-bimodal
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- celldetective/models/segmentation_effectors/ricm-bimodal/training_instructions.json
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  celldetective/models/segmentation_generic/blank
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  celldetective/models/segmentation_targets/blank
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  celldetective/models/signal_detection/blank
{celldetective-1.2.2 → celldetective-1.2.2.post1}/setup.py RENAMED
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  requirements = [str(ir.requirement) for ir in requirements]
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  setup(name='celldetective',
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- version='1.2.2',
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+ version='1.2.2.post1',
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  description='description',
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  long_description=(this_directory / "README.md").read_text(),
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  #long_description=open('README.rst',encoding="utf8").read(),
celldetective-1.2.2/celldetective/models/segmentation_effectors/primNK_cfse/config_input.json DELETED
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- {
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- "channels": [
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- "effector_fluo_channel",
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- "None"
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- ],
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- "diameter": 30.0,
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- "cellprob_threshold": 0.0,
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- "flow_threshold": 0.4,
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- "normalization_percentile": [
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- true,
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- true
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- ],
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- "normalization_clip": [
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- true,
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- true
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- "normalization_values": [
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- [
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- 0.5,
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- 99.0
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- ],
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- [
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- 1.0,
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- 99.0
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- ]
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- ],
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- "model_type": "cellpose",
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- "spatial_calibration": 0.21783999999999998
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- }
celldetective-1.2.2/celldetective/models/segmentation_effectors/primNK_cfse/training_instructions.json DELETED
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- {
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- "model_name": "cp-cfse-transfer",
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- "model_type": "cellpose",
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- "pretrained": "/home/limozin/Documents/GitHub/celldetective/celldetective/models/segmentation_generic/CP_cyto2",
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- "spatial_calibration": 0.21783999999999998,
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- "channel_option": [
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- "effector_fluo_channel",
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- "None"
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- ],
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- "normalization_percentile": [
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- true,
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- true
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- ],
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- "normalization_clip": [
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- true,
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- true
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- ],
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- "normalization_values": [
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- [
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- ],
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- [
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- 1.0,
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- ],
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- "ds": [
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- "/home/limozin/Desktop/primNK_w_MCF7/dataset"
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- ],
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- "augmentation_factor": 1.5,
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- "validation_split": 0.2,
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- "learning_rate": 0.001,
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- "batch_size": 8,
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- "epochs": 3000,
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- "target_directory": "/home/limozin/Documents/GitHub/celldetective/celldetective/models/segmentation_effectors"
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- }
celldetective-1.2.2/celldetective/models/segmentation_effectors/ricm-bimodal/config_input.json DELETED
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- {
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- "channels": [
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- "adhesion_channel",
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- "brightfield_channel"
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- ],
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- "diameter": 30.0,
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- "cellprob_threshold": 0.0,
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- "flow_threshold": 0.4,
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- "normalization_percentile": [
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- false,
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- true
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- ],
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- "normalization_clip": [
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- "normalization_values": [
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- "model_type": "cellpose",
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- "spatial_calibration": 0.2,
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- "dataset": {
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- "train": [
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_100_0109.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/StaticRICM-Dom-20191016-Her2-10nM-C7b21_200_0057.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/StaticRICM-Dom-20191016-Her2-10nM-C7b21_200_0058.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/AdhesionDalia-26-08_209_0022.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/AdhesionDalia-26-08_2015_0039.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Exp20190619_700_0024.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia-2021-04-27_C7b21NF-incub-with-cells-test_605_0037.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_102_0039.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_200_0034.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_103_0011.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_701_0004.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_201_0035.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_100_0016.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia-2021-04-27_C7b21NF-incub-with-cells-test_202_0020.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dominique20191016_303_0016.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_502_0000.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/20231213_RICM_2C11_PP2_normed_201_0000.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_105_0031.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/AdhesionDalia-26-08_2012_0039.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia-2021-04-27_C7b21NF-incub-with-cells-test_608_0028.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_2012_0027.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_101_0021.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia-2021-04-27_C7b21NF-incub-with-cells-test_302_0039.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_104_0036.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_801_0036.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_502_0036.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_808_0173.tif",
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- "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_5011_0006.tif",
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