napari-tmidas 0.3.1__tar.gz → 0.3.2__tar.gz

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  1. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/PKG-INFO +1 -1
  2. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/docs/crop_anything.md +25 -1
  3. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_version.py +3 -3
  4. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas.egg-info/PKG-INFO +1 -1
  5. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/.github/dependabot.yml +0 -0
  6. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/.github/workflows/test_and_deploy.yml +0 -0
  7. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/.gitignore +0 -0
  8. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/.napari-hub/DESCRIPTION.md +0 -0
  9. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/.napari-hub/config.yml +0 -0
  10. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/.pre-commit-config.yaml +0 -0
  11. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/LICENSE +0 -0
  12. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/MANIFEST.in +0 -0
  13. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/README.md +0 -0
  14. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/docs/advanced_processing.md +0 -0
  15. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/docs/basic_processing.md +0 -0
  16. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/docs/careamics_denoising.md +0 -0
  17. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/docs/cellpose_segmentation.md +0 -0
  18. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/docs/file_conversion.md +0 -0
  19. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/docs/grid_view_overlay.md +0 -0
  20. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/docs/intensity_label_filter.md +0 -0
  21. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/docs/regionprops_analysis.md +0 -0
  22. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/docs/regionprops_summary.md +0 -0
  23. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/docs/spotiflow_detection.md +0 -0
  24. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/docs/trackastra_tracking.md +0 -0
  25. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/docs/viscy_virtual_staining.md +0 -0
  26. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/examples/grid_overlay_example.py +0 -0
  27. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/examples/intensity_filter_example.py +0 -0
  28. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/examples/regionprops_example.py +0 -0
  29. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/pyproject.toml +0 -0
  30. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/setup.cfg +0 -0
  31. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/__init__.py +0 -0
  32. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_crop_anything.py +0 -0
  33. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_env_manager.py +0 -0
  34. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_file_conversion.py +0 -0
  35. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_file_selector.py +0 -0
  36. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_label_inspection.py +0 -0
  37. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_processing_worker.py +0 -0
  38. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_reader.py +0 -0
  39. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_registry.py +0 -0
  40. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_roi_colocalization.py +0 -0
  41. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_sample_data.py +0 -0
  42. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_tests/test_crop_anything.py +0 -0
  43. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_tests/test_env_manager.py +0 -0
  44. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_tests/test_file_selector.py +0 -0
  45. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_tests/test_grid_view_overlay.py +0 -0
  46. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_tests/test_init.py +0 -0
  47. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_tests/test_intensity_label_filter.py +0 -0
  48. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_tests/test_label_inspection.py +0 -0
  49. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_tests/test_processing_basic.py +0 -0
  50. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_tests/test_processing_worker.py +0 -0
  51. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_tests/test_reader.py +0 -0
  52. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_tests/test_regionprops_analysis.py +0 -0
  53. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_tests/test_registry.py +0 -0
  54. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_tests/test_sample_data.py +0 -0
  55. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_tests/test_scipy_filters.py +0 -0
  56. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_tests/test_skimage_filters.py +0 -0
  57. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_tests/test_split_channels.py +0 -0
  58. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_tests/test_spotiflow.py +0 -0
  59. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_tests/test_tyx_display_fix.py +0 -0
  60. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_tests/test_ui_utils.py +0 -0
  61. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_tests/test_viscy_virtual_staining.py +0 -0
  62. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_tests/test_widget.py +0 -0
  63. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_tests/test_windows_basic.py +0 -0
  64. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_tests/test_writer.py +0 -0
  65. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_ui_utils.py +0 -0
  66. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_widget.py +0 -0
  67. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_writer.py +0 -0
  68. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/napari.yaml +0 -0
  69. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/processing_functions/__init__.py +0 -0
  70. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/processing_functions/basic.py +0 -0
  71. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/processing_functions/careamics_denoising.py +0 -0
  72. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/processing_functions/careamics_env_manager.py +0 -0
  73. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/processing_functions/cellpose_env_manager.py +0 -0
  74. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/processing_functions/cellpose_segmentation.py +0 -0
  75. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/processing_functions/colocalization.py +0 -0
  76. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/processing_functions/file_compression.py +0 -0
  77. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/processing_functions/grid_view_overlay.py +0 -0
  78. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/processing_functions/intensity_label_filter.py +0 -0
  79. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/processing_functions/regionprops_analysis.py +0 -0
  80. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/processing_functions/sam2_env_manager.py +0 -0
  81. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/processing_functions/sam2_mp4.py +0 -0
  82. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/processing_functions/scipy_filters.py +0 -0
  83. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/processing_functions/skimage_filters.py +0 -0
  84. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/processing_functions/spotiflow_detection.py +0 -0
  85. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/processing_functions/spotiflow_env_manager.py +0 -0
  86. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/processing_functions/timepoint_merger.py +0 -0
  87. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/processing_functions/trackastra_tracking.py +0 -0
  88. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/processing_functions/viscy_env_manager.py +0 -0
  89. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/processing_functions/viscy_virtual_staining.py +0 -0
  90. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas.egg-info/SOURCES.txt +0 -0
  91. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas.egg-info/dependency_links.txt +0 -0
  92. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas.egg-info/entry_points.txt +0 -0
  93. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas.egg-info/requires.txt +0 -0
  94. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas.egg-info/top_level.txt +0 -0
  95. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/test_grid_overlay.py +0 -0
  96. {napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/tox.ini +0 -0
{napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: napari-tmidas
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- Version: 0.3.1
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+ Version: 0.3.2
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  Summary: A plugin for batch processing of confocal and whole-slide microscopy images of biological tissues
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  Author: Marco Meer
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  Author-email: marco.meer@pm.me
{napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/docs/crop_anything.md RENAMED
@@ -94,13 +94,37 @@ The plugin automatically detects your data format:
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  ## Interactive Controls
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- ### Point Prompts
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+ ### Prompt Modes
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+
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+ SAM2 supports two ways to specify objects:
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+
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+ #### Point Mode (Default)
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+ Click on image to add point prompts. Best for complex boundaries or small objects.
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  | Action | Effect |
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  |--------|--------|
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  | **Click** | Add positive point (include this region) |
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  | **Shift+Click** | Add negative point (exclude this region) |
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+
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+ #### Box Mode
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+ Draw rectangles around objects. Best for quick segmentation of simple objects.
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+
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+ 1. Select **Box Mode** from the UI
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+ 2. Draw rectangle around object
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+ 3. SAM2 segments the region inside the box
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+ 4. Can add more rectangles for multiple objects
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+ 5. Shift+draw to refine/subtract from existing box
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+
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+ **When to use each:**
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+ - **Points**: Fine details, intricate boundaries, removing noise
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+ - **Box**: Quick segmentation, well-defined rectangular regions, speed
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+
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+ ### Navigation
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+
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+ | Action | Effect |
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+ |--------|--------|
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  | **Left/Right Click** | Navigate to adjacent frames (3D mode) |
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+ | **Dimension Slider** | Jump to specific frame/slice (3D mode) |
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  ### Table Selection
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{napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas/_version.py RENAMED
@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
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  commit_id: COMMIT_ID
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  __commit_id__: COMMIT_ID
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- __version__ = version = '0.3.1'
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- __version_tuple__ = version_tuple = (0, 3, 1)
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+ __version__ = version = '0.3.2'
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+ __version_tuple__ = version_tuple = (0, 3, 2)
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- __commit_id__ = commit_id = 'g17da1f7b4'
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+ __commit_id__ = commit_id = 'gfa06bb8df'
{napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/src/napari_tmidas.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: napari-tmidas
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- Version: 0.3.1
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+ Version: 0.3.2
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  Summary: A plugin for batch processing of confocal and whole-slide microscopy images of biological tissues
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  Author: Marco Meer
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  Author-email: marco.meer@pm.me
{napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/.gitignore RENAMED
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{napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/LICENSE RENAMED
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{napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/MANIFEST.in RENAMED
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{napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/README.md RENAMED
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{napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/setup.cfg RENAMED
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{napari_tmidas-0.3.1 → napari_tmidas-0.3.2}/tox.ini RENAMED
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