napari-tmidas 0.1.1__tar.gz → 0.1.3__tar.gz

{napari_tmidas-0.1.1 → napari_tmidas-0.1.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: napari-tmidas
-Version: 0.1.1
+Version: 0.1.3
 Summary: Tissue Microscopy Image Data Analysis Suite
 Author: Marco Meer
 Author-email: marco.meer@pm.me
@@ -57,6 +57,7 @@ Requires-Dist: numpy
 Requires-Dist: magicgui
 Requires-Dist: qtpy
 Requires-Dist: scikit-image
+Requires-Dist: pyqt5
 Provides-Extra: testing
 Requires-Dist: tox; extra == "testing"
 Requires-Dist: pytest; extra == "testing"
@@ -71,34 +72,54 @@ Requires-Dist: pyqt5; extra == "testing"
 [![PyPI](https://img.shields.io/pypi/v/napari-tmidas.svg?color=green)](https://pypi.org/project/napari-tmidas)
 [![Python Version](https://img.shields.io/pypi/pyversions/napari-tmidas.svg?color=green)](https://python.org)
 [![tests](https://github.com/macromeer/napari-tmidas/workflows/tests/badge.svg)](https://github.com/macromeer/napari-tmidas/actions)
-[![codecov](https://codecov.io/gh/macromeer/napari-tmidas/branch/main/graph/badge.svg)](https://codecov.io/gh/macromeer/napari-tmidas)
 [![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-tmidas)](https://napari-hub.org/plugins/napari-tmidas)
+<!-- [![codecov](https://codecov.io/gh/macromeer/napari-tmidas/branch/main/graph/badge.svg)](https://codecov.io/gh/macromeer/napari-tmidas) -->
 
-Tissue Microscopy Image Data Analysis Suite
+The Tissue Microscopy Image Data Analysis Suite (short: T-MIDAS), is a collection of pipelines for batch image preprocessing, segmentation, regions-of-interest (ROI) analysis and other useful features. This 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).
 
-----------------------------------
+## Installation
 
-This [napari] plugin was generated with [copier] using the [napari-plugin-template].
+First install Napari in a virtual environment following the latest [Napari installation instructions](https://github.com/Napari/napari?tab=readme-ov-file#installation).
 
-<!--
-Don't miss the full getting started guide to set up your new package:
-https://github.com/napari/napari-plugin-template#getting-started
 
-and review the napari docs for plugin developers:
-https://napari.org/stable/plugins/index.html
--->
+After you have activated the environment, you can install `napari-tmidas` via [pip]:
 
-## Installation
+    pip install napari-tmidas
 
-You can install `napari-tmidas` via [pip]:
+To install the latest development version:
 
-    pip install napari-tmidas
+    pip install git+https://github.com/macromeer/napari-tmidas.git
 
+## Usage
 
+You can find the installed plugin here:
+   
+![image](https://github.com/user-attachments/assets/504db09a-d66e-49eb-90cd-3237024d9d7a)
 
-To install latest development version :
+### File inspector
 
-    pip install git+https://github.com/macromeer/napari-tmidas.git
+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.
+   
+![image](https://github.com/user-attachments/assets/41ecb689-9abe-4371-83b5-9c5eb37069f9)
+
+2. As a result, a table appears with the found images.
+   
+![image](https://github.com/user-attachments/assets/8360942a-be8f-49ec-bc25-385ee43bd601)
+
+3. Next, select a processing function, set parameters if applicable and `Start Batch Processing`.
+   
+![image](https://github.com/user-attachments/assets/05929660-6672-4f76-89da-4f17749ccfad)
+
+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. 
+    
+![image](https://github.com/user-attachments/assets/cfe84828-c1cc-4196-9a53-5dfb82d5bfce)
+
+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. 
+
+### Label inspector
+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).
+
+![image](https://github.com/user-attachments/assets/0bf8c6ae-4212-449d-8183-e91b23ba740e)
 
 
 ## Contributing
@@ -128,6 +149,18 @@ If you encounter any problems, please [file an issue] along with a detailed desc
 
 [file an issue]: https://github.com/macromeer/napari-tmidas/issues
 
+----------------------------------
+
+This [napari] plugin was generated with [copier] using the [napari-plugin-template].
+
+<!--
+Don't miss the full getting started guide to set up your new package:
+https://github.com/napari/napari-plugin-template#getting-started
+
+and review the napari docs for plugin developers:
+https://napari.org/stable/plugins/index.html
+-->
+
 [napari]: https://github.com/napari/napari
 [tox]: https://tox.readthedocs.io/en/latest/
 [pip]: https://pypi.org/project/pip/

napari_tmidas-0.1.3/README.md

@@ -0,0 +1,99 @@
+# napari-tmidas
+
+[![License BSD-3](https://img.shields.io/pypi/l/napari-tmidas.svg?color=green)](https://github.com/macromeer/napari-tmidas/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/napari-tmidas.svg?color=green)](https://pypi.org/project/napari-tmidas)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-tmidas.svg?color=green)](https://python.org)
+[![tests](https://github.com/macromeer/napari-tmidas/workflows/tests/badge.svg)](https://github.com/macromeer/napari-tmidas/actions)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-tmidas)](https://napari-hub.org/plugins/napari-tmidas)
+<!-- [![codecov](https://codecov.io/gh/macromeer/napari-tmidas/branch/main/graph/badge.svg)](https://codecov.io/gh/macromeer/napari-tmidas) -->
+
+The Tissue Microscopy Image Data Analysis Suite (short: T-MIDAS), is a collection of pipelines for batch image preprocessing, segmentation, regions-of-interest (ROI) analysis and other useful features. This 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).
+
+## Installation
+
+First install Napari in a virtual environment following the latest [Napari installation instructions](https://github.com/Napari/napari?tab=readme-ov-file#installation).
+
+
+After you have activated the environment, you can install `napari-tmidas` via [pip]:
+
+    pip install napari-tmidas
+
+To install the latest development version:
+
+    pip install git+https://github.com/macromeer/napari-tmidas.git
+
+## Usage
+
+You can find the installed plugin here:
+   
+![image](https://github.com/user-attachments/assets/504db09a-d66e-49eb-90cd-3237024d9d7a)
+
+### File inspector
+
+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.
+   
+![image](https://github.com/user-attachments/assets/41ecb689-9abe-4371-83b5-9c5eb37069f9)
+
+2. As a result, a table appears with the found images.
+   
+![image](https://github.com/user-attachments/assets/8360942a-be8f-49ec-bc25-385ee43bd601)
+
+3. Next, select a processing function, set parameters if applicable and `Start Batch Processing`.
+   
+![image](https://github.com/user-attachments/assets/05929660-6672-4f76-89da-4f17749ccfad)
+
+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. 
+    
+![image](https://github.com/user-attachments/assets/cfe84828-c1cc-4196-9a53-5dfb82d5bfce)
+
+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. 
+
+### Label inspector
+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).
+
+![image](https://github.com/user-attachments/assets/0bf8c6ae-4212-449d-8183-e91b23ba740e)
+
+
+## Contributing
+
+Contributions are very welcome. Tests can be run with [tox], please ensure
+the coverage at least stays the same before you submit a pull request.
+
+## License
+
+Distributed under the terms of the [BSD-3] license,
+"napari-tmidas" is free and open source software
+
+## Issues
+
+If you encounter any problems, please [file an issue] along with a detailed description.
+
+[napari]: https://github.com/napari/napari
+[copier]: https://copier.readthedocs.io/en/stable/
+[@napari]: https://github.com/napari
+[MIT]: http://opensource.org/licenses/MIT
+[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
+[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
+[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
+[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
+[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
+[napari-plugin-template]: https://github.com/napari/napari-plugin-template
+
+[file an issue]: https://github.com/macromeer/napari-tmidas/issues
+
+----------------------------------
+
+This [napari] plugin was generated with [copier] using the [napari-plugin-template].
+
+<!--
+Don't miss the full getting started guide to set up your new package:
+https://github.com/napari/napari-plugin-template#getting-started
+
+and review the napari docs for plugin developers:
+https://napari.org/stable/plugins/index.html
+-->
+
+[napari]: https://github.com/napari/napari
+[tox]: https://tox.readthedocs.io/en/latest/
+[pip]: https://pypi.org/project/pip/
+[PyPI]: https://pypi.org/

{napari_tmidas-0.1.1 → napari_tmidas-0.1.3}/pyproject.toml

@@ -29,6 +29,7 @@ dependencies = [
     "magicgui",
     "qtpy",
     "scikit-image",
+    "pyqt5",
 ]
 
 [project.optional-dependencies]

{napari_tmidas-0.1.1 → napari_tmidas-0.1.3}/src/napari_tmidas/__init__.py

@@ -3,14 +3,10 @@ try:
 except ImportError:
     __version__ = "unknown"
 
+
+from ._label_inspection import label_inspector_widget
 from ._reader import napari_get_reader
 from ._sample_data import make_sample_data
-from ._widget import (
-    ExampleQWidget,
-    ImageThreshold,
-    threshold_autogenerate_widget,
-    threshold_magic_widget,
-)
 from ._writer import write_multiple, write_single_image
 
 __all__ = (
@@ -18,8 +14,6 @@ __all__ = (
     "write_single_image",
     "write_multiple",
     "make_sample_data",
-    "ExampleQWidget",
-    "ImageThreshold",
-    "threshold_autogenerate_widget",
-    "threshold_magic_widget",
+    "file_selector",
+    "label_inspector_widget",
 )