napari-tmidas 0.2.5__tar.gz → 0.2.6__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 (88) hide show
  1. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/PKG-INFO +3 -7
  2. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/README.md +2 -6
  3. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_version.py +3 -3
  4. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas.egg-info/PKG-INFO +3 -7
  5. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/.github/dependabot.yml +0 -0
  6. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/.github/workflows/test_and_deploy.yml +0 -0
  7. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/.gitignore +0 -0
  8. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/.napari-hub/DESCRIPTION.md +0 -0
  9. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/.napari-hub/config.yml +0 -0
  10. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/.pre-commit-config.yaml +0 -0
  11. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/LICENSE +0 -0
  12. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/MANIFEST.in +0 -0
  13. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/docs/advanced_processing.md +0 -0
  14. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/docs/basic_processing.md +0 -0
  15. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/docs/cellpose_segmentation.md +0 -0
  16. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/docs/grid_view_overlay.md +0 -0
  17. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/docs/intensity_label_filter.md +0 -0
  18. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/docs/regionprops_analysis.md +0 -0
  19. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/docs/regionprops_summary.md +0 -0
  20. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/docs/trackastra_tracking.md +0 -0
  21. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/examples/grid_overlay_example.py +0 -0
  22. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/examples/intensity_filter_example.py +0 -0
  23. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/examples/regionprops_example.py +0 -0
  24. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/pyproject.toml +0 -0
  25. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/setup.cfg +0 -0
  26. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/__init__.py +0 -0
  27. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_crop_anything.py +0 -0
  28. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_env_manager.py +0 -0
  29. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_file_conversion.py +0 -0
  30. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_file_selector.py +0 -0
  31. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_label_inspection.py +0 -0
  32. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_processing_worker.py +0 -0
  33. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_reader.py +0 -0
  34. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_registry.py +0 -0
  35. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_roi_colocalization.py +0 -0
  36. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_sample_data.py +0 -0
  37. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_crop_anything.py +0 -0
  38. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_env_manager.py +0 -0
  39. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_file_selector.py +0 -0
  40. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_grid_view_overlay.py +0 -0
  41. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_init.py +0 -0
  42. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_intensity_label_filter.py +0 -0
  43. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_label_inspection.py +0 -0
  44. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_processing_basic.py +0 -0
  45. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_processing_worker.py +0 -0
  46. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_reader.py +0 -0
  47. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_regionprops_analysis.py +0 -0
  48. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_registry.py +0 -0
  49. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_sample_data.py +0 -0
  50. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_scipy_filters.py +0 -0
  51. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_skimage_filters.py +0 -0
  52. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_split_channels.py +0 -0
  53. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_spotiflow.py +0 -0
  54. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_tyx_display_fix.py +0 -0
  55. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_ui_utils.py +0 -0
  56. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_widget.py +0 -0
  57. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_windows_basic.py +0 -0
  58. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_writer.py +0 -0
  59. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_ui_utils.py +0 -0
  60. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_widget.py +0 -0
  61. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_writer.py +0 -0
  62. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/napari.yaml +0 -0
  63. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/__init__.py +0 -0
  64. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/basic.py +0 -0
  65. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/careamics_denoising.py +0 -0
  66. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/careamics_env_manager.py +0 -0
  67. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/cellpose_env_manager.py +0 -0
  68. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/cellpose_segmentation.py +0 -0
  69. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/colocalization.py +0 -0
  70. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/file_compression.py +0 -0
  71. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/grid_view_overlay.py +0 -0
  72. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/intensity_label_filter.py +0 -0
  73. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/regionprops_analysis.py +0 -0
  74. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/sam2_env_manager.py +0 -0
  75. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/sam2_mp4.py +0 -0
  76. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/scipy_filters.py +0 -0
  77. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/skimage_filters.py +0 -0
  78. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/spotiflow_detection.py +0 -0
  79. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/spotiflow_env_manager.py +0 -0
  80. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/timepoint_merger.py +0 -0
  81. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/trackastra_tracking.py +0 -0
  82. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas.egg-info/SOURCES.txt +0 -0
  83. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas.egg-info/dependency_links.txt +0 -0
  84. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas.egg-info/entry_points.txt +0 -0
  85. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas.egg-info/requires.txt +0 -0
  86. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas.egg-info/top_level.txt +0 -0
  87. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/test_grid_overlay.py +0 -0
  88. {napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/tox.ini +0 -0
{napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: napari-tmidas
3
- Version: 0.2.5
3
+ Version: 0.2.6
4
4
  Summary: A plugin for batch processing of confocal and whole-slide microscopy images of biological tissues
5
5
  Author: Marco Meer
6
6
  Author-email: marco.meer@pm.me
@@ -132,13 +132,9 @@ It is recommended though to install the **latest development version**. Please a
132
132
 
133
133
  ### Additional Setup for Batch Crop Anything
134
134
 
135
- To use the Batch Crop Anything pipeline with SAM2, you need to install SAM2 separately:
135
+ To use the Batch Crop Anything pipeline with SAM2, you only need to install ffmpeg manually. SAM2 and its model checkpoints will be automatically installed when you first run the pipeline:
136
136
 
137
- cd /opt # if the folder does not exist: mkdir /opt && cd /opt
138
- git clone https://github.com/facebookresearch/sam2.git && cd sam2
139
- pip install -e .
140
- curl -L https://dl.fbaipublicfiles.com/segment_anything_2/092824/sam2.1_hiera_large.pt -o checkpoints/sam2.1_hiera_large.pt
141
- mamba install -c conda-forge ffmpeg # we also need ffmpeg
137
+ mamba install -c conda-forge ffmpeg
142
138
 
143
139
  If you want to batch compress image data using [Zstandard](https://github.com/facebook/zstd), use the package manager of your operating system to install it:
144
140
 
{napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/README.md RENAMED
@@ -40,13 +40,9 @@ It is recommended though to install the **latest development version**. Please a
40
40
 
41
41
  ### Additional Setup for Batch Crop Anything
42
42
 
43
- To use the Batch Crop Anything pipeline with SAM2, you need to install SAM2 separately:
43
+ To use the Batch Crop Anything pipeline with SAM2, you only need to install ffmpeg manually. SAM2 and its model checkpoints will be automatically installed when you first run the pipeline:
44
44
 
45
- cd /opt # if the folder does not exist: mkdir /opt && cd /opt
46
- git clone https://github.com/facebookresearch/sam2.git && cd sam2
47
- pip install -e .
48
- curl -L https://dl.fbaipublicfiles.com/segment_anything_2/092824/sam2.1_hiera_large.pt -o checkpoints/sam2.1_hiera_large.pt
49
- mamba install -c conda-forge ffmpeg # we also need ffmpeg
45
+ mamba install -c conda-forge ffmpeg
50
46
 
51
47
  If you want to batch compress image data using [Zstandard](https://github.com/facebook/zstd), use the package manager of your operating system to install it:
52
48
 
{napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas/_version.py RENAMED
@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
28
28
  commit_id: COMMIT_ID
29
29
  __commit_id__: COMMIT_ID
30
30
 
31
- __version__ = version = '0.2.5'
32
- __version_tuple__ = version_tuple = (0, 2, 5)
31
+ __version__ = version = '0.2.6'
32
+ __version_tuple__ = version_tuple = (0, 2, 6)
33
33
 
34
- __commit_id__ = commit_id = 'g707181b75'
34
+ __commit_id__ = commit_id = 'gff20a16be'
{napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/src/napari_tmidas.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: napari-tmidas
3
- Version: 0.2.5
3
+ Version: 0.2.6
4
4
  Summary: A plugin for batch processing of confocal and whole-slide microscopy images of biological tissues
5
5
  Author: Marco Meer
6
6
  Author-email: marco.meer@pm.me
@@ -132,13 +132,9 @@ It is recommended though to install the **latest development version**. Please a
132
132
 
133
133
  ### Additional Setup for Batch Crop Anything
134
134
 
135
- To use the Batch Crop Anything pipeline with SAM2, you need to install SAM2 separately:
135
+ To use the Batch Crop Anything pipeline with SAM2, you only need to install ffmpeg manually. SAM2 and its model checkpoints will be automatically installed when you first run the pipeline:
136
136
 
137
- cd /opt # if the folder does not exist: mkdir /opt && cd /opt
138
- git clone https://github.com/facebookresearch/sam2.git && cd sam2
139
- pip install -e .
140
- curl -L https://dl.fbaipublicfiles.com/segment_anything_2/092824/sam2.1_hiera_large.pt -o checkpoints/sam2.1_hiera_large.pt
141
- mamba install -c conda-forge ffmpeg # we also need ffmpeg
137
+ mamba install -c conda-forge ffmpeg
142
138
 
143
139
  If you want to batch compress image data using [Zstandard](https://github.com/facebook/zstd), use the package manager of your operating system to install it:
144
140
 
{napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/.gitignore RENAMED
File without changes
{napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/LICENSE RENAMED
File without changes
{napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/MANIFEST.in RENAMED
File without changes
{napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/setup.cfg RENAMED
File without changes
{napari_tmidas-0.2.5 → napari_tmidas-0.2.6}/tox.ini RENAMED
File without changes