napari-tmidas 0.1.3__tar.gz → 0.1.5__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.
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/PKG-INFO +35 -12
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/README.md +32 -10
- napari_tmidas-0.1.5/src/napari_tmidas/_file_conversion.py +1706 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/src/napari_tmidas/_file_selector.py +357 -60
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/src/napari_tmidas/_label_inspection.py +87 -26
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/src/napari_tmidas/_version.py +2 -2
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/src/napari_tmidas/napari.yaml +9 -4
- napari_tmidas-0.1.5/src/napari_tmidas/processing_functions/basic.py +42 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/src/napari_tmidas/processing_functions/skimage_filters.py +60 -43
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/src/napari_tmidas.egg-info/PKG-INFO +35 -12
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/src/napari_tmidas.egg-info/SOURCES.txt +1 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/tox.ini +8 -1
- napari_tmidas-0.1.3/src/napari_tmidas/processing_functions/basic.py +0 -60
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/.github/dependabot.yml +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/.github/workflows/test_and_deploy.yml +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/.gitignore +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/.napari-hub/DESCRIPTION.md +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/.napari-hub/config.yml +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/.pre-commit-config.yaml +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/LICENSE +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/MANIFEST.in +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/pyproject.toml +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/setup.cfg +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/src/napari_tmidas/__init__.py +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/src/napari_tmidas/_reader.py +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/src/napari_tmidas/_registry.py +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/src/napari_tmidas/_sample_data.py +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/src/napari_tmidas/_tests/__init__.py +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/src/napari_tmidas/_tests/test_reader.py +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/src/napari_tmidas/_tests/test_sample_data.py +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/src/napari_tmidas/_tests/test_widget.py +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/src/napari_tmidas/_tests/test_writer.py +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/src/napari_tmidas/_widget.py +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/src/napari_tmidas/_writer.py +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/src/napari_tmidas/processing_functions/__init__.py +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/src/napari_tmidas/processing_functions/scipy_filters.py +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/src/napari_tmidas.egg-info/dependency_links.txt +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/src/napari_tmidas.egg-info/entry_points.txt +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/src/napari_tmidas.egg-info/requires.txt +0 -0
- {napari_tmidas-0.1.3 → napari_tmidas-0.1.5}/src/napari_tmidas.egg-info/top_level.txt +0 -0
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Metadata-Version: 2.
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Metadata-Version: 2.4
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Name: napari-tmidas
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Version: 0.1.
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Version: 0.1.5
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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
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Requires-Dist: pytest-qt; extra == "testing"
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Requires-Dist: napari; extra == "testing"
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Requires-Dist: pyqt5; extra == "testing"
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Dynamic: license-file
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# napari-tmidas
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[](https://github.com/macromeer/napari-tmidas/actions)
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[](https://napari-hub.org/plugins/napari-tmidas)
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<!-- [](https://codecov.io/gh/macromeer/napari-tmidas) -->
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This Napari plugin allows you to perform batch image processing without a graphics processing unit (GPU). It will still be fast because computations will run in parallel on your central processing unit (CPU).
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This plugin provides you with a growing collection of pipelines for batch image preprocessing, segmentation, regions-of-interest (ROI) analysis and other useful features.
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`napari-tmidas` is a work in progress (WIP) and an evolutionary step away from the [terminal / command-line version of T-MIDAS](https://github.com/MercaderLabAnatomy/T-MIDAS).
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## Installation
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First install Napari in a virtual environment
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First install Napari in a virtual environment:
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mamba create -y -n napari-tmidas -c conda-forge python=3.11 tqdm
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mamba activate napari-tmidas
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python -m pip install "napari[all]"
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Now you can install `napari-tmidas` via [pip]:
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pip install napari-tmidas
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pip install git+https://github.com/macromeer/napari-tmidas.git
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### Dependencies
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For the File converter, we need some libraries to read some microscopy formats and to write ome-zarr:
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pip install nd2 readlif tiffslide pylibCZIrw acquifer-napari ome-zarr
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## Usage
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You can find the installed plugin here:
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### File converter
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You might first want to batch convert microscopy image data. Currently, this plugin supports `.nd2, .lif, .ndpi, .czi` and acquifer data. After launching the file converter, you can scan a folder of your choice for microscopy image data. It will also detect series images that you can preview. Start by selecting an original image in the first column of the table. This allows you to preview or convert.
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### File inspector
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1. After opening `Plugins > T-MIDAS > File selector`, 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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2. As a result, a table appears with the found images.
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3. Next, select a processing function, set parameters if applicable and `Start Batch Processing`.
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4. You can click on the images in the table to show them in the viewer. For example first click on one of the `Original Files`, and then the corresponding `Processed File` to see an overlay.
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4. You can click on the images in the table to show them in the viewer. For example first click on one of the `Original Files`, and then the corresponding `Processed File` to see an overlay.
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Note that whenever you click on an `Original File` or `Processed File` in the table, it will replace the one that is currently shown in the viewer. So naturally, you'd first select the original image, and then the processed image to correctly see the image pair that you want to inspect.
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Note that whenever you click on an `Original File` or `Processed File` in the table, it will replace the one that is currently shown in the viewer. So naturally, you'd first select the original image, and then the processed image to correctly see the image pair that you want to inspect.
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### Label inspector
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If you have already segmented a folder full of images and now you want to maybe inspect and edit each label image, you can use the `Plugins > T-MIDAS > Label inspector`, which automatically saves your changes to the existing label image once you click the `Save Changes and Continue` button (bottom right).
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## Contributing
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Contributions are very welcome. Tests can be run with [tox], please ensure
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[](https://github.com/macromeer/napari-tmidas/actions)
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[](https://napari-hub.org/plugins/napari-tmidas)
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<!-- [](https://codecov.io/gh/macromeer/napari-tmidas) -->
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This Napari plugin allows you to perform batch image processing without a graphics processing unit (GPU). It will still be fast because computations will run in parallel on your central processing unit (CPU).
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This plugin provides you with a growing collection of pipelines for batch image preprocessing, segmentation, regions-of-interest (ROI) analysis and other useful features.
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`napari-tmidas` is a work in progress (WIP) and an evolutionary step away from the [terminal / command-line version of T-MIDAS](https://github.com/MercaderLabAnatomy/T-MIDAS).
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## Installation
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First install Napari in a virtual environment:
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mamba create -y -n napari-tmidas -c conda-forge python=3.11 tqdm
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mamba activate napari-tmidas
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python -m pip install "napari[all]"
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Now you can install `napari-tmidas` via [pip]:
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pip install napari-tmidas
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pip install git+https://github.com/macromeer/napari-tmidas.git
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### Dependencies
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For the File converter, we need some libraries to read some microscopy formats and to write ome-zarr:
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pip install nd2 readlif tiffslide pylibCZIrw acquifer-napari ome-zarr
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## Usage
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You can find the installed plugin here:
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### File converter
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You might first want to batch convert microscopy image data. Currently, this plugin supports `.nd2, .lif, .ndpi, .czi` and acquifer data. After launching the file converter, you can scan a folder of your choice for microscopy image data. It will also detect series images that you can preview. Start by selecting an original image in the first column of the table. This allows you to preview or convert.
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### File inspector
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1. After opening `Plugins > T-MIDAS > File selector`, 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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2. As a result, a table appears with the found images.
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3. Next, select a processing function, set parameters if applicable and `Start Batch Processing`.
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4. You can click on the images in the table to show them in the viewer. For example first click on one of the `Original Files`, and then the corresponding `Processed File` to see an overlay.
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4. You can click on the images in the table to show them in the viewer. For example first click on one of the `Original Files`, and then the corresponding `Processed File` to see an overlay.
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Note that whenever you click on an `Original File` or `Processed File` in the table, it will replace the one that is currently shown in the viewer. So naturally, you'd first select the original image, and then the processed image to correctly see the image pair that you want to inspect.
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Note that whenever you click on an `Original File` or `Processed File` in the table, it will replace the one that is currently shown in the viewer. So naturally, you'd first select the original image, and then the processed image to correctly see the image pair that you want to inspect.
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### Label inspector
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If you have already segmented a folder full of images and now you want to maybe inspect and edit each label image, you can use the `Plugins > T-MIDAS > Label inspector`, which automatically saves your changes to the existing label image once you click the `Save Changes and Continue` button (bottom right).
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## Contributing
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Contributions are very welcome. Tests can be run with [tox], please ensure
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