napari-tmidas 0.1.7__tar.gz → 0.1.8__tar.gz

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Files changed (42) hide show
  1. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/PKG-INFO +14 -10
  2. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/README.md +13 -9
  3. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas/_version.py +2 -2
  4. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas.egg-info/PKG-INFO +14 -10
  5. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/.github/dependabot.yml +0 -0
  6. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/.github/workflows/test_and_deploy.yml +0 -0
  7. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/.gitignore +0 -0
  8. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/.napari-hub/DESCRIPTION.md +0 -0
  9. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/.napari-hub/config.yml +0 -0
  10. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/.pre-commit-config.yaml +0 -0
  11. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/LICENSE +0 -0
  12. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/MANIFEST.in +0 -0
  13. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/pyproject.toml +0 -0
  14. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/setup.cfg +0 -0
  15. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas/__init__.py +0 -0
  16. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas/_crop_anything.py +0 -0
  17. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas/_file_conversion.py +0 -0
  18. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas/_file_selector.py +0 -0
  19. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas/_label_inspection.py +0 -0
  20. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas/_reader.py +0 -0
  21. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas/_registry.py +0 -0
  22. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas/_roi_colocalization.py +0 -0
  23. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas/_sample_data.py +0 -0
  24. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas/_tests/__init__.py +0 -0
  25. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas/_tests/test_reader.py +0 -0
  26. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas/_tests/test_sample_data.py +0 -0
  27. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas/_tests/test_widget.py +0 -0
  28. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas/_tests/test_writer.py +0 -0
  29. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas/_widget.py +0 -0
  30. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas/_writer.py +0 -0
  31. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas/napari.yaml +0 -0
  32. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas/processing_functions/__init__.py +0 -0
  33. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas/processing_functions/basic.py +0 -0
  34. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas/processing_functions/colocalization.py +0 -0
  35. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas/processing_functions/scipy_filters.py +0 -0
  36. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas/processing_functions/skimage_filters.py +0 -0
  37. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas.egg-info/SOURCES.txt +0 -0
  38. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas.egg-info/dependency_links.txt +0 -0
  39. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas.egg-info/entry_points.txt +0 -0
  40. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas.egg-info/requires.txt +0 -0
  41. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas.egg-info/top_level.txt +0 -0
  42. {napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/tox.ini +0 -0
{napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/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: 0.1.7
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+ Version: 0.1.8
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  Summary: Tissue Microscopy Image Data Analysis Suite
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  Author: Marco Meer
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  Author-email: marco.meer@pm.me
@@ -79,20 +79,19 @@ The `napari-tmidas` plugin consists of a growing collection of pipelines for fas
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  ## Feature Overview
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- ### Current Pipelines
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- 1. **Batch Image Processing**
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+ 1. **Image Processing**
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  - Process image folders with: Gamma correction, Z-projection, channel splitting, Gaussian/median filters, thresholding (Otsu/manual), and label cleaning
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- 2. **Batch Label Inspection**
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+ 2. **Label Inspection**
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  - Review and edit label images with auto-save
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- 3. **Batch Microscopy Image Conversion**
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+ 3. **Microscopy Image Conversion**
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  - Convert .nd2/.lif/.ndpi/.czi/acquifer → .tif/.zarr with metadata preservation
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- 4. **Batch Crop Anything**
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+ 4. **Crop Anything**
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  - Interactive ROI selection via click interface
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- 5. Batch ROI Colocalization
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+ 5. **ROI Colocalization**
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  - Count colocalized labels across multiple channels
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@@ -138,13 +137,13 @@ You can find the installed plugin here:
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  ![image](https://github.com/user-attachments/assets/504db09a-d66e-49eb-90cd-3237024d9d7a)
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- ### Batch Microscopy Image Conversion
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+ ### Microscopy Image Conversion
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  You can start this pipeline via `Plugins > T-MIDAS > Batch Microscopy Image Conversion`. Currently, this pipeline supports the conversion of `.nd2, .lif, .ndpi, .czi` and acquifer data. After scanning a folder of your choice for microscopy image data, select a file in the first column of the table and preview and export any image data it contains.
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  ![image](https://github.com/user-attachments/assets/e377ca71-2f30-447d-825e-d2feebf7061b)
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- ### Batch File Processing
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+ ### Image Processing
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  1. After opening `Plugins > T-MIDAS > Batch Image Processing`, enter the path to the folder containing the images to be processed (currently supports TIF, later also ZARR). You can also filter for filename suffix.
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@@ -169,11 +168,16 @@ If you have already segmented a folder full of images and now you want to maybe
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  ![image](https://github.com/user-attachments/assets/0bf8c6ae-4212-449d-8183-e91b23ba740e)
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- ### Batch Crop Anything
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+ ### Crop Anything
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  This pipeline combines the Segment Anything Model (SAM) for automatic object detection with an interactive interface for selecting and cropping multiple objects from images. To launch the widget, open `Plugins > T-MIDAS > Batch Crop Anything`
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  ![image](https://github.com/user-attachments/assets/6d72c2a2-1064-4a27-b398-a9b86fcbc443)
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+ ### ROI Colocalization
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+ This pipeline quantifies colocalization between labeled regions of interest (ROIs) across multiple image channels. It determines the extent of overlap between ROIs in a reference channel and those in one or two other channels. The output is a table of colocalization counts. Optionally, the size of reference channel ROIs, as well as the total or median size of colocalizing ROIs in the other channels, can be included. Colocalization is determined using Boolean masking. The number of colocalizing instances is determined by counting unique label IDs within the overlapping regions. Typically, the reference channel contains larger structures, while other channels contain smaller, potentially nested, structures. For example, the reference channel might contain cell bodies, with the second and third channels containing nuclei and sub-nuclear objects, respectively.
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+
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+ ![napari-tmidas_coloc_pipeline](https://github.com/user-attachments/assets/2f9022a0-7b88-4588-a448-250f07a634d7)
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+
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  ## Contributing
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{napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/README.md RENAMED
@@ -10,20 +10,19 @@ The `napari-tmidas` plugin consists of a growing collection of pipelines for fas
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  ## Feature Overview
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12
 
13
- ### Current Pipelines
14
- 1. **Batch Image Processing**
13
+ 1. **Image Processing**
15
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  - Process image folders with: Gamma correction, Z-projection, channel splitting, Gaussian/median filters, thresholding (Otsu/manual), and label cleaning
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- 2. **Batch Label Inspection**
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+ 2. **Label Inspection**
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  - Review and edit label images with auto-save
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20
- 3. **Batch Microscopy Image Conversion**
19
+ 3. **Microscopy Image Conversion**
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20
  - Convert .nd2/.lif/.ndpi/.czi/acquifer → .tif/.zarr with metadata preservation
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- 4. **Batch Crop Anything**
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+ 4. **Crop Anything**
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  - Interactive ROI selection via click interface
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- 5. Batch ROI Colocalization
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+ 5. **ROI Colocalization**
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  - Count colocalized labels across multiple channels
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@@ -69,13 +68,13 @@ You can find the installed plugin here:
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  ![image](https://github.com/user-attachments/assets/504db09a-d66e-49eb-90cd-3237024d9d7a)
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- ### Batch Microscopy Image Conversion
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+ ### Microscopy Image Conversion
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  You can start this pipeline via `Plugins > T-MIDAS > Batch Microscopy Image Conversion`. Currently, this pipeline supports the conversion of `.nd2, .lif, .ndpi, .czi` and acquifer data. After scanning a folder of your choice for microscopy image data, select a file in the first column of the table and preview and export any image data it contains.
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  ![image](https://github.com/user-attachments/assets/e377ca71-2f30-447d-825e-d2feebf7061b)
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- ### Batch File Processing
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+ ### Image Processing
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  1. After opening `Plugins > T-MIDAS > Batch Image Processing`, enter the path to the folder containing the images to be processed (currently supports TIF, later also ZARR). You can also filter for filename suffix.
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@@ -100,11 +99,16 @@ If you have already segmented a folder full of images and now you want to maybe
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  ![image](https://github.com/user-attachments/assets/0bf8c6ae-4212-449d-8183-e91b23ba740e)
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- ### Batch Crop Anything
102
+ ### Crop Anything
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  This pipeline combines the Segment Anything Model (SAM) for automatic object detection with an interactive interface for selecting and cropping multiple objects from images. To launch the widget, open `Plugins > T-MIDAS > Batch Crop Anything`
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  ![image](https://github.com/user-attachments/assets/6d72c2a2-1064-4a27-b398-a9b86fcbc443)
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+ ### ROI Colocalization
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+ This pipeline quantifies colocalization between labeled regions of interest (ROIs) across multiple image channels. It determines the extent of overlap between ROIs in a reference channel and those in one or two other channels. The output is a table of colocalization counts. Optionally, the size of reference channel ROIs, as well as the total or median size of colocalizing ROIs in the other channels, can be included. Colocalization is determined using Boolean masking. The number of colocalizing instances is determined by counting unique label IDs within the overlapping regions. Typically, the reference channel contains larger structures, while other channels contain smaller, potentially nested, structures. For example, the reference channel might contain cell bodies, with the second and third channels containing nuclei and sub-nuclear objects, respectively.
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+
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+ ![napari-tmidas_coloc_pipeline](https://github.com/user-attachments/assets/2f9022a0-7b88-4588-a448-250f07a634d7)
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+
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  ## Contributing
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{napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/src/napari_tmidas/_version.py RENAMED
@@ -17,5 +17,5 @@ __version__: str
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  __version_tuple__: VERSION_TUPLE
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  version_tuple: VERSION_TUPLE
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- __version__ = version = '0.1.7'
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- __version_tuple__ = version_tuple = (0, 1, 7)
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+ __version__ = version = '0.1.8'
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+ __version_tuple__ = version_tuple = (0, 1, 8)
{napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/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: 0.1.7
3
+ Version: 0.1.8
4
4
  Summary: Tissue Microscopy Image Data Analysis Suite
5
5
  Author: Marco Meer
6
6
  Author-email: marco.meer@pm.me
@@ -79,20 +79,19 @@ The `napari-tmidas` plugin consists of a growing collection of pipelines for fas
79
79
 
80
80
  ## Feature Overview
81
81
 
82
- ### Current Pipelines
83
- 1. **Batch Image Processing**
82
+ 1. **Image Processing**
84
83
  - Process image folders with: Gamma correction, Z-projection, channel splitting, Gaussian/median filters, thresholding (Otsu/manual), and label cleaning
85
84
 
86
- 2. **Batch Label Inspection**
85
+ 2. **Label Inspection**
87
86
  - Review and edit label images with auto-save
88
87
 
89
- 3. **Batch Microscopy Image Conversion**
88
+ 3. **Microscopy Image Conversion**
90
89
  - Convert .nd2/.lif/.ndpi/.czi/acquifer → .tif/.zarr with metadata preservation
91
90
 
92
- 4. **Batch Crop Anything**
91
+ 4. **Crop Anything**
93
92
  - Interactive ROI selection via click interface
94
93
 
95
- 5. Batch ROI Colocalization
94
+ 5. **ROI Colocalization**
96
95
  - Count colocalized labels across multiple channels
97
96
 
98
97
 
@@ -138,13 +137,13 @@ You can find the installed plugin here:
138
137
  ![image](https://github.com/user-attachments/assets/504db09a-d66e-49eb-90cd-3237024d9d7a)
139
138
 
140
139
 
141
- ### Batch Microscopy Image Conversion
140
+ ### Microscopy Image Conversion
142
141
 
143
142
  You can start this pipeline via `Plugins > T-MIDAS > Batch Microscopy Image Conversion`. Currently, this pipeline supports the conversion of `.nd2, .lif, .ndpi, .czi` and acquifer data. After scanning a folder of your choice for microscopy image data, select a file in the first column of the table and preview and export any image data it contains.
144
143
 
145
144
  ![image](https://github.com/user-attachments/assets/e377ca71-2f30-447d-825e-d2feebf7061b)
146
145
 
147
- ### Batch File Processing
146
+ ### Image Processing
148
147
 
149
148
  1. After opening `Plugins > T-MIDAS > Batch Image Processing`, enter the path to the folder containing the images to be processed (currently supports TIF, later also ZARR). You can also filter for filename suffix.
150
149
 
@@ -169,11 +168,16 @@ If you have already segmented a folder full of images and now you want to maybe
169
168
 
170
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  ![image](https://github.com/user-attachments/assets/0bf8c6ae-4212-449d-8183-e91b23ba740e)
171
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172
- ### Batch Crop Anything
171
+ ### Crop Anything
173
172
  This pipeline combines the Segment Anything Model (SAM) for automatic object detection with an interactive interface for selecting and cropping multiple objects from images. To launch the widget, open `Plugins > T-MIDAS > Batch Crop Anything`
174
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175
174
  ![image](https://github.com/user-attachments/assets/6d72c2a2-1064-4a27-b398-a9b86fcbc443)
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176
+ ### ROI Colocalization
177
+ This pipeline quantifies colocalization between labeled regions of interest (ROIs) across multiple image channels. It determines the extent of overlap between ROIs in a reference channel and those in one or two other channels. The output is a table of colocalization counts. Optionally, the size of reference channel ROIs, as well as the total or median size of colocalizing ROIs in the other channels, can be included. Colocalization is determined using Boolean masking. The number of colocalizing instances is determined by counting unique label IDs within the overlapping regions. Typically, the reference channel contains larger structures, while other channels contain smaller, potentially nested, structures. For example, the reference channel might contain cell bodies, with the second and third channels containing nuclei and sub-nuclear objects, respectively.
178
+
179
+ ![napari-tmidas_coloc_pipeline](https://github.com/user-attachments/assets/2f9022a0-7b88-4588-a448-250f07a634d7)
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+
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  ## Contributing
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{napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/.gitignore RENAMED
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{napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/LICENSE RENAMED
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{napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/MANIFEST.in RENAMED
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{napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/setup.cfg RENAMED
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{napari_tmidas-0.1.7 → napari_tmidas-0.1.8}/tox.ini RENAMED
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