napari-tmidas 0.2.4__tar.gz → 0.2.6__tar.gz

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Files changed (88) hide show
  1. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/PKG-INFO +4 -7
  2. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/README.md +3 -6
  3. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_version.py +3 -3
  4. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas.egg-info/PKG-INFO +4 -7
  5. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/.github/dependabot.yml +0 -0
  6. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/.github/workflows/test_and_deploy.yml +0 -0
  7. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/.gitignore +0 -0
  8. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/.napari-hub/DESCRIPTION.md +0 -0
  9. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/.napari-hub/config.yml +0 -0
  10. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/.pre-commit-config.yaml +0 -0
  11. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/LICENSE +0 -0
  12. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/MANIFEST.in +0 -0
  13. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/docs/advanced_processing.md +0 -0
  14. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/docs/basic_processing.md +0 -0
  15. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/docs/cellpose_segmentation.md +0 -0
  16. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/docs/grid_view_overlay.md +0 -0
  17. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/docs/intensity_label_filter.md +0 -0
  18. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/docs/regionprops_analysis.md +0 -0
  19. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/docs/regionprops_summary.md +0 -0
  20. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/docs/trackastra_tracking.md +0 -0
  21. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/examples/grid_overlay_example.py +0 -0
  22. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/examples/intensity_filter_example.py +0 -0
  23. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/examples/regionprops_example.py +0 -0
  24. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/pyproject.toml +0 -0
  25. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/setup.cfg +0 -0
  26. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/__init__.py +0 -0
  27. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_crop_anything.py +0 -0
  28. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_env_manager.py +0 -0
  29. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_file_conversion.py +0 -0
  30. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_file_selector.py +0 -0
  31. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_label_inspection.py +0 -0
  32. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_processing_worker.py +0 -0
  33. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_reader.py +0 -0
  34. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_registry.py +0 -0
  35. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_roi_colocalization.py +0 -0
  36. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_sample_data.py +0 -0
  37. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_crop_anything.py +0 -0
  38. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_env_manager.py +0 -0
  39. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_file_selector.py +0 -0
  40. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_grid_view_overlay.py +0 -0
  41. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_init.py +0 -0
  42. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_intensity_label_filter.py +0 -0
  43. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_label_inspection.py +0 -0
  44. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_processing_basic.py +0 -0
  45. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_processing_worker.py +0 -0
  46. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_reader.py +0 -0
  47. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_regionprops_analysis.py +0 -0
  48. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_registry.py +0 -0
  49. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_sample_data.py +0 -0
  50. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_scipy_filters.py +0 -0
  51. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_skimage_filters.py +0 -0
  52. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_split_channels.py +0 -0
  53. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_spotiflow.py +0 -0
  54. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_tyx_display_fix.py +0 -0
  55. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_ui_utils.py +0 -0
  56. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_widget.py +0 -0
  57. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_windows_basic.py +0 -0
  58. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_tests/test_writer.py +0 -0
  59. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_ui_utils.py +0 -0
  60. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_widget.py +0 -0
  61. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_writer.py +0 -0
  62. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/napari.yaml +0 -0
  63. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/__init__.py +0 -0
  64. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/basic.py +0 -0
  65. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/careamics_denoising.py +0 -0
  66. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/careamics_env_manager.py +0 -0
  67. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/cellpose_env_manager.py +0 -0
  68. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/cellpose_segmentation.py +0 -0
  69. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/colocalization.py +0 -0
  70. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/file_compression.py +0 -0
  71. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/grid_view_overlay.py +0 -0
  72. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/intensity_label_filter.py +0 -0
  73. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/regionprops_analysis.py +0 -0
  74. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/sam2_env_manager.py +0 -0
  75. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/sam2_mp4.py +0 -0
  76. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/scipy_filters.py +0 -0
  77. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/skimage_filters.py +0 -0
  78. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/spotiflow_detection.py +0 -0
  79. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/spotiflow_env_manager.py +0 -0
  80. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/timepoint_merger.py +0 -0
  81. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/processing_functions/trackastra_tracking.py +0 -0
  82. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas.egg-info/SOURCES.txt +0 -0
  83. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas.egg-info/dependency_links.txt +0 -0
  84. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas.egg-info/entry_points.txt +0 -0
  85. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas.egg-info/requires.txt +0 -0
  86. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas.egg-info/top_level.txt +0 -0
  87. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/test_grid_overlay.py +0 -0
  88. {napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/tox.ini +0 -0
{napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/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: 0.2.4
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+ Version: 0.2.6
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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
@@ -96,6 +96,7 @@ Dynamic: license-file
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  [![PyPI](https://img.shields.io/pypi/v/napari-tmidas.svg?color=green)](https://pypi.org/project/napari-tmidas)
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  [![Python Version](https://img.shields.io/pypi/pyversions/napari-tmidas.svg?color=green)](https://python.org)
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  [![Downloads](https://static.pepy.tech/badge/napari-tmidas)](https://pepy.tech/project/napari-tmidas)
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+ [![DOI](https://zenodo.org/badge/698257324.svg)](https://zenodo.org/badge/latestdoi/698257324)
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  [![tests](https://github.com/macromeer/napari-tmidas/workflows/tests/badge.svg)](https://github.com/macromeer/napari-tmidas/actions)
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  This napari plugin consists of a growing collection of pipelines for fast batch processing of confocal and whole slide microscopy images of biological tissues. This is a WIP and based on the [T-MIDAS terminal](https://github.com/MercaderLabAnatomy/T-MIDAS).
@@ -131,13 +132,9 @@ It is recommended though to install the **latest development version**. Please a
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  ### Additional Setup for Batch Crop Anything
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- To use the Batch Crop Anything pipeline with SAM2, you need to install SAM2 separately:
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+ 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:
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- cd /opt # if the folder does not exist: mkdir /opt && cd /opt
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- git clone https://github.com/facebookresearch/sam2.git && cd sam2
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- pip install -e .
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- curl -L https://dl.fbaipublicfiles.com/segment_anything_2/092824/sam2.1_hiera_large.pt -o checkpoints/sam2.1_hiera_large.pt
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- mamba install -c conda-forge ffmpeg # we also need ffmpeg
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+ mamba install -c conda-forge ffmpeg
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  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:
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{napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/README.md RENAMED
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  [![PyPI](https://img.shields.io/pypi/v/napari-tmidas.svg?color=green)](https://pypi.org/project/napari-tmidas)
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  [![Python Version](https://img.shields.io/pypi/pyversions/napari-tmidas.svg?color=green)](https://python.org)
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  [![Downloads](https://static.pepy.tech/badge/napari-tmidas)](https://pepy.tech/project/napari-tmidas)
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+ [![DOI](https://zenodo.org/badge/698257324.svg)](https://zenodo.org/badge/latestdoi/698257324)
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  [![tests](https://github.com/macromeer/napari-tmidas/workflows/tests/badge.svg)](https://github.com/macromeer/napari-tmidas/actions)
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  This napari plugin consists of a growing collection of pipelines for fast batch processing of confocal and whole slide microscopy images of biological tissues. This is a WIP and based on the [T-MIDAS terminal](https://github.com/MercaderLabAnatomy/T-MIDAS).
@@ -39,13 +40,9 @@ It is recommended though to install the **latest development version**. Please a
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  ### Additional Setup for Batch Crop Anything
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- To use the Batch Crop Anything pipeline with SAM2, you need to install SAM2 separately:
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+ 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:
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- cd /opt # if the folder does not exist: mkdir /opt && cd /opt
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- git clone https://github.com/facebookresearch/sam2.git && cd sam2
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- pip install -e .
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- curl -L https://dl.fbaipublicfiles.com/segment_anything_2/092824/sam2.1_hiera_large.pt -o checkpoints/sam2.1_hiera_large.pt
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- mamba install -c conda-forge ffmpeg # we also need ffmpeg
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+ mamba install -c conda-forge ffmpeg
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  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:
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{napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/src/napari_tmidas/_version.py RENAMED
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- __version__ = version = '0.2.4'
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- __version_tuple__ = version_tuple = (0, 2, 4)
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+ __version__ = version = '0.2.6'
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+ __version_tuple__ = version_tuple = (0, 2, 6)
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- __commit_id__ = commit_id = 'gfdc22d5dc'
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+ __commit_id__ = commit_id = 'gff20a16be'
{napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/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: 0.2.4
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+ Version: 0.2.6
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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
@@ -96,6 +96,7 @@ Dynamic: license-file
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  [![PyPI](https://img.shields.io/pypi/v/napari-tmidas.svg?color=green)](https://pypi.org/project/napari-tmidas)
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  [![Python Version](https://img.shields.io/pypi/pyversions/napari-tmidas.svg?color=green)](https://python.org)
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  [![Downloads](https://static.pepy.tech/badge/napari-tmidas)](https://pepy.tech/project/napari-tmidas)
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+ [![DOI](https://zenodo.org/badge/698257324.svg)](https://zenodo.org/badge/latestdoi/698257324)
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  [![tests](https://github.com/macromeer/napari-tmidas/workflows/tests/badge.svg)](https://github.com/macromeer/napari-tmidas/actions)
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  This napari plugin consists of a growing collection of pipelines for fast batch processing of confocal and whole slide microscopy images of biological tissues. This is a WIP and based on the [T-MIDAS terminal](https://github.com/MercaderLabAnatomy/T-MIDAS).
@@ -131,13 +132,9 @@ It is recommended though to install the **latest development version**. Please a
131
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132
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  ### Additional Setup for Batch Crop Anything
133
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134
- 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:
135
136
 
136
- cd /opt # if the folder does not exist: mkdir /opt && cd /opt
137
- git clone https://github.com/facebookresearch/sam2.git && cd sam2
138
- pip install -e .
139
- curl -L https://dl.fbaipublicfiles.com/segment_anything_2/092824/sam2.1_hiera_large.pt -o checkpoints/sam2.1_hiera_large.pt
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- mamba install -c conda-forge ffmpeg # we also need ffmpeg
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+ mamba install -c conda-forge ffmpeg
141
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  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:
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{napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/.gitignore RENAMED
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{napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/LICENSE RENAMED
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{napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/MANIFEST.in RENAMED
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{napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/setup.cfg RENAMED
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{napari_tmidas-0.2.4 → napari_tmidas-0.2.6}/tox.ini RENAMED
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