BrainLesion · neuronflow · Aug 23, 2025 · Aug 7, 2025 · Aug 9, 2025 · Aug 9, 2025
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -66,10 +66,10 @@ please specify your docker version, You can find it by running:
 docker --version
 ```
 
-### Version of !PACKAGE_NAME! ?
-please specify your version of !PACKAGE_NAME! (please make sure you run the latest version):
+### Version of !stroke_segmentor! ?
+please specify your version of !stroke_segmentor! (please make sure you run the latest version):
 ```sh
-pip freeze | grep !PACKAGE_NAME!
+pip freeze | grep !stroke_segmentor!
 ```
 
 **Additional context**

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -16,7 +16,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest] #, windows-latest, macos-latest] # Extend to your needs
-        python-version: ["3.10", "3.11", "3.12"] # Extend to your needs
+        python-version: ["3.9","3.10", "3.11", "3.12", "3.13"] # Extend to your needs
 
     steps:
       - uses: actions/checkout@v4
@@ -39,7 +39,7 @@ jobs:
           poetry run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
       - name: Test with pytest
         run: |
-          poetry run pytest --cov=package_name --cov-report=xml --cov-report=term
+          poetry run pytest --cov=stroke_segmentor --cov-report=xml --cov-report=term
       # Add the following block to upload coverage to Codecov, requires a CODECOV_TOKEN secret to be set in the repository
       # - name: Upload results to Codecov
       #   # Only upload to Codecov after a merge to the main branch

diff --git a/.gitignore b/.gitignore
@@ -158,3 +158,11 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+testdata
+NVAUTO
+*.nii.gz
+*.ipynb
+.vscode
+
+stroke_segmentor/weights
diff --git a/Makefile b/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/README.md b/README.md
@@ -1,22 +1,21 @@
-# PACKAGE_NAME
+# Stroke Segmentor
 
-[![Python Versions](https://img.shields.io/pypi/pyversions/PACKAGE_NAME)](https://pypi.org/project/PACKAGE_NAME/)
-[![Stable Version](https://img.shields.io/pypi/v/PACKAGE_NAME?label=stable)](https://pypi.python.org/pypi/PACKAGE_NAME/)
-[![Documentation Status](https://readthedocs.org/projects/PACKAGE_NAME/badge/?version=latest)](http://PACKAGE_NAME.readthedocs.io/?badge=latest)
-[![tests](https://github.com/BrainLesion/PACKAGE_NAME/actions/workflows/tests.yml/badge.svg)](https://github.com/BrainLesion/PACKAGE_NAME/actions/workflows/tests.yml)
-[![codecov](https://codecov.io/gh/BrainLesion/PACKAGE_NAME/graph/badge.svg?token=A7FWUKO9Y4)](https://codecov.io/gh/BrainLesion/PACKAGE_NAME)
+[![Python Versions](https://img.shields.io/pypi/pyversions/stroke_segmentor)](https://pypi.org/project/stroke_segmentor/)
+[![Stable Version](https://img.shields.io/pypi/v/stroke_segmentor?label=stable)](https://pypi.python.org/pypi/stroke_segmentor/)
+[![Documentation Status](https://readthedocs.org/projects/stroke_segmentor/badge/?version=latest)](http://stroke_segmentor.readthedocs.io/?badge=latest)
+[![tests](https://github.com/BrainLesion/stroke_segmentor/actions/workflows/tests.yml/badge.svg)](https://github.com/BrainLesion/stroke_segmentor/actions/workflows/tests.yml)
 [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+<!-- [![codecov](https://codecov.io/gh/BrainLesion/stroke_segmentor/graph/badge.svg?token=A7FWUKO9Y4)](https://codecov.io/gh/BrainLesion/stroke_segmentor) -->
 
-Description 
-## Features
+State-of-the-art ischemic stroke lesion segmentation in MRI
 
 
 ## Installation
 
-With a Python 3.8+ environment, you can install `PACKAGE_NAME` directly from [PyPI](https://pypi.org/project/PACKAGE_NAME/):
+With a Python 3.8+ environment, you can install `stroke_segmentor` directly from [PyPI](https://pypi.org/project/stroke_segmentor/):
 
 ```bash
-pip install PACKAGE_NAME
+pip install stroke_segmentor
 ```
 
 
@@ -25,27 +24,33 @@ pip install PACKAGE_NAME
 A minimal example to create a segmentation could look like this:
 
 ```python
-    # example
+from stroke_segmentor.inferer import Inferer
+
+inferer = Inferer()
+pred = inferer.infer(
+    dwi_path="path/to/dwi.nii.gz",
+    adc_path="path/to/adc.nii.gz",
+    segmentation_path="seg.nii.gz", # optional. the numpy array is always returned for direct usage
+)
 ```
 
-<!-- For more examples and details please refer to our extensive Notebook tutorials here [NBViewer](https://nbviewer.org/github/BrainLesion/tutorials/blob/main/PACKAGE_NAME/tutorial.ipynb) ([GitHub](https://github.com/BrainLesion/tutorials/blob/main/PACKAGE_NAME/tutorial.ipynb)). For the best experience open the notebook in Colab. -->
-
-
 ## Citation
 
-If you use PACKAGE_NAME in your research, please cite it to support the development!
+> [!IMPORTANT]
+> `stroke_segmentor` is part of the [BrainLesion](https://github.com/BrainLesion) suite.  
+> Please cite it support the development!  
+> https://github.com/BrainLesion#-citing-brainlesion-suite
 
-```
-TODO: citation will be added asap
-```
+ This project is based on [DeepISLES](https://github.com/ezequieldlrosa/DeepIsles) and offers its NVAUTO algorithm.
+ Please cite the [original manuscript](https://github.com/ezequieldlrosa/DeepIsles?tab=readme-ov-file#citations).
 
 ## Contributing
 
 We welcome all kinds of contributions from the community!
 
 ### Reporting Bugs, Feature Requests and Questions
 
-Please open a new issue [here](https://github.com/BrainLesion/PACKAGE_NAME/issues).
+Please open a new issue [here](https://github.com/BrainLesion/stroke_segmentor/issues).
 
 ### Code contributions
 

diff --git a/docs/README_preprocessed.md b/docs/README_preprocessed.md
@@ -0,0 +1,57 @@
+# Stroke Segmentor
+
+[![Python Versions](https://img.shields.io/pypi/pyversions/stroke_segmentor)](https://pypi.org/project/stroke_segmentor/)
+[![Stable Version](https://img.shields.io/pypi/v/stroke_segmentor?label=stable)](https://pypi.python.org/pypi/stroke_segmentor/)
+[![Documentation Status](https://readthedocs.org/projects/stroke_segmentor/badge/?version=latest)](http://stroke_segmentor.readthedocs.io/?badge=latest)
+[![tests](https://github.com/BrainLesion/stroke_segmentor/actions/workflows/tests.yml/badge.svg)](https://github.com/BrainLesion/stroke_segmentor/actions/workflows/tests.yml)
+[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+<!-- [![codecov](https://codecov.io/gh/BrainLesion/stroke_segmentor/graph/badge.svg?token=A7FWUKO9Y4)](https://codecov.io/gh/BrainLesion/stroke_segmentor) -->
+
+State-of-the-art ischemic stroke lesion segmentation in MRI
+
+
+## Installation
+
+With a Python 3.8+ environment, you can install `stroke_segmentor` directly from [PyPI](https://pypi.org/project/stroke_segmentor/):
+
+```bash
+pip install stroke_segmentor
+```
+
+
+## Use Cases and Tutorials
+
+A minimal example to create a segmentation could look like this:
+
+```python
+from stroke_segmentor.inferer import Inferer
+
+inferer = Inferer()
+pred = inferer.infer(
+    dwi_path="path/to/dwi.nii.gz",
+    adc_path="path/to/adc.nii.gz",
+    segmentation_path="seg.nii.gz", # optional. the numpy array is always returned for direct usage
+)
+```
+
+## Citation
+
+```{IMPORTANT}
+`stroke_segmentor` is part of the [BrainLesion](https://github.com/BrainLesion) suite.  
+Please cite it support the development!  
+https://github.com/BrainLesion#-citing-brainlesion-suite
+```
+ This project is based on [DeepISLES](https://github.com/ezequieldlrosa/DeepIsles) and offers its NVAUTO algorithm.
+ Please cite the [original manuscript](https://github.com/ezequieldlrosa/DeepIsles?tab=readme-ov-file#citations).
+
+## Contributing
+
+We welcome all kinds of contributions from the community!
+
+### Reporting Bugs, Feature Requests and Questions
+
+Please open a new issue [here](https://github.com/BrainLesion/stroke_segmentor/issues).
+
+### Code contributions
+
+Nice to have you on board! Please have a look at our [CONTRIBUTING.md](CONTRIBUTING.md) file.
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -16,8 +16,8 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = "PACKAGE_NAME"
-copyright = "2024, Marcel Rosier et al."
+project = "stroke_segmentor"
+copyright = "2025, Marcel Rosier et al."
 author = "Marcel Rosier, Florian Kofler"
 
 # -- General configuration ---------------------------------------------------

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -1,4 +1,4 @@
-PACKAGE_NAME documentation
+stroke_segmentor documentation
 ===================
 
 .. include:: ../README_preprocessed.md
@@ -20,3 +20,6 @@ Sections
    :maxdepth: 2
    :caption: API Reference:
 
+   inferer
+   model_handler
+
diff --git a/docs/source/inferer.rst b/docs/source/inferer.rst
@@ -0,0 +1,5 @@
+Inferer
+===================
+
+.. automodule:: stroke_segmentor.inferer
+   :members:
diff --git a/docs/source/model_handler.rst b/docs/source/model_handler.rst
@@ -0,0 +1,5 @@
+Model Handler
+===================
+
+.. automodule:: stroke_segmentor.model_handler
+   :members:
diff --git a/make.bat b/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/package_name/__init__.py b/package_name/__init__.py