seqseg 0.1.0__tar.gz

seqseg-0.1.0/LICENSE

@@ -0,0 +1,201 @@
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seqseg-0.1.0/PKG-INFO

@@ -0,0 +1,174 @@
+Metadata-Version: 2.4
+Name: seqseg
+Version: 0.1.0
+Summary: A simple deep learning-based medical image blood vessel tracking and segmentation tool.
+Author: Shadden Lab, UC Berkeley
+Author-email: Numi Sveinsson Cepero <numi@berkeley.com>
+License: Apache-2.0
+Project-URL: homepage, https://github.com/numisveinsson/SeqSeg
+Project-URL: repository, https://github.com/numisveinsson/SeqSeg
+Keywords: segmentation,deep learning,medical imaging,nnunet,medical image analysis,medical image segmentation,nnU-Net,blood vessel segmentation,vascular segmentation,vascular tracking
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: vtk
+Requires-Dist: SimpleITK
+Requires-Dist: PyYAML
+Requires-Dist: nnunetv2
+Dynamic: license-file
+
+![example workflow](https://github.com/numisveinsson/SeqSeg/actions/workflows/python-app.yml/badge.svg)
+
+# SeqSeg: Automatic Tracking and Segmentation of Blood Vessels in CT and MR Images
+
+See paper [here](https://rdcu.be/dU0wy) for detailed explanations and citation.
+
+Below is an example showing the algorithm tracking and segmenting an abdominal aorta in 3D MR image scan:
+
+![](seqseg/assets/mr_model_tracing_fast_shorter.gif)
+
+## How it works
+SeqSeg is a method for automatic tracking and segmentation of blood vessels in medical images. The algorithm uses a neural network to segment the vasculature locally and uses a tracking algorithm to take steps along the direction of the vessel and down bifurcation detected.
+
+Here is the workflow of the algorithm:
+
+![](assets/seqseg.png)
+
+where the neural network was trained on local subvolume patches of the image:
+
+![](assets/seqseg_training.png)
+
+## Set Up
+SeqSeg relies on [nnU-Net](https://github.com/MIC-DKFZ/nnUNet) for segmentation of the local medical image volumes. You will need model weights to run the algorithm - either use pretrained weights (available) or train a model yourself. After training a nnU-Net model, the weights will be saved in a `nnUNet_results` folder.
+
+Main package dependencies:
+
+Basic:
+- Python 3.11
+
+Machine Learning (Note: must be installed according to nnU-Net instructions):
+- nnU-Net, nnunetv2=2.5.1
+- Pytorch, torch=2.3.1
+
+Image and Data Processing:
+- SITK, simpleitk=2.2.1
+- VTK, vtk=9.1.0
+- PyYaml, pyyaml=6.0.1
+- Matplotlib (optional)
+- Pyyaml (optional)
+
+and if using VMTK (not required):
+- VMTK
+
+Example setup using conda:
+```bash
+conda create -n seqseg python=3.11
+conda activate seqseg
+conda install ..
+```
+Example setup using pip (first create a virtual environment, see [here](https://packaging.python.org/en/latest/guides/installing-using-pip-and-virtual-environments/)):
+```bash
+python3 -m venv seqseg
+source seqseg/bin/activate
+pip install python==3.11
+pip install ...
+```
+Note: The code is tested with Python 3.11 and nnU-Net 2.5.1. If you are using a different version, please check the compatibility of the packages.
+
+## Testing
+
+Current workflow:
+1. Create conda or virtual environment and install ''Image and Data Processing'' dependencies.
+2. Test this environment using the test script tests/test.sh
+3. Install nnunet and pytorch using the instructions [here](https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/installation_instructions.md).
+4. Try the full installation according to details below
+
+## Running
+
+See [here](https://github.com/numisveinsson/SeqSeg/blob/main/tutorial/tutorial.md) for tutorial on how to run the code.
+
+### Set weights directory
+```bash
+export nnUNet_results="/path/to/model/weights/nnUnet/nnUNet_results"
+```
+
+### Activate environment (eg. conda)
+```bash
+conda activate seqseg
+```
+
+### Run
+```bash
+python3 seqseg.py --data_dir data --test_name 3d_fullres --train_dataset Dataset001_AORTAS --config_name global.yml --fold all --img_ext .nii.gz --outdir output --scale 1 --start 0 --stop -1 --max_n_steps 1000 --unit cm
+```
+
+### Details
+
+`seqseg`: Main script to run.
+
+Arguments:
+
+-`data_dir`: This argument specifies the name of the folder containing the testing data (and test.json if applicable).
+
+-`test_name`: This argument specifies the name of the nnUNet test to use. The default value is '3d_fullres'. Other possible values could be '2d', etc.
+
+-`train_dataset`: This argument specifies the name of the dataset used to train the nnUNet model. For example, 'Dataset010_SEQCOROASOCACT'.
+
+-'config_name': This argument specifies the name of the config file to use. The default value is 'global.yml'.
+
+-`fold`: This argument specifies which fold to use for the nnUNet model. The default value is 'all'.
+
+-`img_ext`: This argument specifies the image extension. For example, '.nii.gz'.
+
+-`outdir`: This argument specifies the output directory where the results will be saved.
+
+-`scale`: This argument specifies whether to scale image data. This is needed if the units for the nnUNet model and testing data are different. The default value is 1.
+
+-`start`: This argument specifies where to start in the list of testing samples. The default value is 0.
+
+-`stop`: This argument specifies where to stop in the list of testing samples. The default value is -1, which means to process all samples until the end of the list.
+
+-`max_n_steps`: This argument specifies the maximum number of steps to run the algorithm. The default value is 1000.
+
+-`unit`: This argument specifies the unit of the image data. The default value is 'cm'.
+
+Data directory: Assumes the following structure:
+- Directory
+    - images
+    - centerlines (if applicable)
+    - truths (if applicable)
+    - test.json (if applicable)
+
+SeqSeg requires a seed point for initialization. This can be given by either:
+- test.json file: located in data directory (see sample under data)
+- centerline: if centerlines are given, we initialize using the first points of the centerline
+- cardiac mesh: then the aortic valve must be labeled as Region 8 and LV 7
+
+## Config file
+`config/global.yml`: File contains config parameters, default is set but can be changed depending on task
+
+We recommend duplicating the file and changing the name to avoid overwriting the default values.
+If so, the config file must be passed as an argument when running the script: `config_name`
+
+## Citation
+When using SeqSeg, please cite the following [paper](https://rdcu.be/dU0wy):
+    
+```
+@Article{SveinssonCepero2024,
+author={Sveinsson Cepero, Numi
+and Shadden, Shawn C.},
+title={SeqSeg: Learning Local Segments for Automatic Vascular Model Construction},
+journal={Annals of Biomedical Engineering},
+year={2024},
+month={Sep},
+day={18},
+issn={1573-9686},
+doi={10.1007/s10439-024-03611-z},
+url={https://doi.org/10.1007/s10439-024-03611-z},
+}
+```

seqseg-0.1.0/README.md

@@ -0,0 +1,150 @@
+![example workflow](https://github.com/numisveinsson/SeqSeg/actions/workflows/python-app.yml/badge.svg)
+
+# SeqSeg: Automatic Tracking and Segmentation of Blood Vessels in CT and MR Images
+
+See paper [here](https://rdcu.be/dU0wy) for detailed explanations and citation.
+
+Below is an example showing the algorithm tracking and segmenting an abdominal aorta in 3D MR image scan:
+
+![](seqseg/assets/mr_model_tracing_fast_shorter.gif)
+
+## How it works
+SeqSeg is a method for automatic tracking and segmentation of blood vessels in medical images. The algorithm uses a neural network to segment the vasculature locally and uses a tracking algorithm to take steps along the direction of the vessel and down bifurcation detected.
+
+Here is the workflow of the algorithm:
+
+![](assets/seqseg.png)
+
+where the neural network was trained on local subvolume patches of the image:
+
+![](assets/seqseg_training.png)
+
+## Set Up
+SeqSeg relies on [nnU-Net](https://github.com/MIC-DKFZ/nnUNet) for segmentation of the local medical image volumes. You will need model weights to run the algorithm - either use pretrained weights (available) or train a model yourself. After training a nnU-Net model, the weights will be saved in a `nnUNet_results` folder.
+
+Main package dependencies:
+
+Basic:
+- Python 3.11
+
+Machine Learning (Note: must be installed according to nnU-Net instructions):
+- nnU-Net, nnunetv2=2.5.1
+- Pytorch, torch=2.3.1
+
+Image and Data Processing:
+- SITK, simpleitk=2.2.1
+- VTK, vtk=9.1.0
+- PyYaml, pyyaml=6.0.1
+- Matplotlib (optional)
+- Pyyaml (optional)
+
+and if using VMTK (not required):
+- VMTK
+
+Example setup using conda:
+```bash
+conda create -n seqseg python=3.11
+conda activate seqseg
+conda install ..
+```
+Example setup using pip (first create a virtual environment, see [here](https://packaging.python.org/en/latest/guides/installing-using-pip-and-virtual-environments/)):
+```bash
+python3 -m venv seqseg
+source seqseg/bin/activate
+pip install python==3.11
+pip install ...
+```
+Note: The code is tested with Python 3.11 and nnU-Net 2.5.1. If you are using a different version, please check the compatibility of the packages.
+
+## Testing
+
+Current workflow:
+1. Create conda or virtual environment and install ''Image and Data Processing'' dependencies.
+2. Test this environment using the test script tests/test.sh
+3. Install nnunet and pytorch using the instructions [here](https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/installation_instructions.md).
+4. Try the full installation according to details below
+
+## Running
+
+See [here](https://github.com/numisveinsson/SeqSeg/blob/main/tutorial/tutorial.md) for tutorial on how to run the code.
+
+### Set weights directory
+```bash
+export nnUNet_results="/path/to/model/weights/nnUnet/nnUNet_results"
+```
+
+### Activate environment (eg. conda)
+```bash
+conda activate seqseg
+```
+
+### Run
+```bash
+python3 seqseg.py --data_dir data --test_name 3d_fullres --train_dataset Dataset001_AORTAS --config_name global.yml --fold all --img_ext .nii.gz --outdir output --scale 1 --start 0 --stop -1 --max_n_steps 1000 --unit cm
+```
+
+### Details
+
+`seqseg`: Main script to run.
+
+Arguments:
+
+-`data_dir`: This argument specifies the name of the folder containing the testing data (and test.json if applicable).
+
+-`test_name`: This argument specifies the name of the nnUNet test to use. The default value is '3d_fullres'. Other possible values could be '2d', etc.
+
+-`train_dataset`: This argument specifies the name of the dataset used to train the nnUNet model. For example, 'Dataset010_SEQCOROASOCACT'.
+
+-'config_name': This argument specifies the name of the config file to use. The default value is 'global.yml'.
+
+-`fold`: This argument specifies which fold to use for the nnUNet model. The default value is 'all'.
+
+-`img_ext`: This argument specifies the image extension. For example, '.nii.gz'.
+
+-`outdir`: This argument specifies the output directory where the results will be saved.
+
+-`scale`: This argument specifies whether to scale image data. This is needed if the units for the nnUNet model and testing data are different. The default value is 1.
+
+-`start`: This argument specifies where to start in the list of testing samples. The default value is 0.
+
+-`stop`: This argument specifies where to stop in the list of testing samples. The default value is -1, which means to process all samples until the end of the list.
+
+-`max_n_steps`: This argument specifies the maximum number of steps to run the algorithm. The default value is 1000.
+
+-`unit`: This argument specifies the unit of the image data. The default value is 'cm'.
+
+Data directory: Assumes the following structure:
+- Directory
+    - images
+    - centerlines (if applicable)
+    - truths (if applicable)
+    - test.json (if applicable)
+
+SeqSeg requires a seed point for initialization. This can be given by either:
+- test.json file: located in data directory (see sample under data)
+- centerline: if centerlines are given, we initialize using the first points of the centerline
+- cardiac mesh: then the aortic valve must be labeled as Region 8 and LV 7
+
+## Config file
+`config/global.yml`: File contains config parameters, default is set but can be changed depending on task
+
+We recommend duplicating the file and changing the name to avoid overwriting the default values.
+If so, the config file must be passed as an argument when running the script: `config_name`
+
+## Citation
+When using SeqSeg, please cite the following [paper](https://rdcu.be/dU0wy):
+    
+```
+@Article{SveinssonCepero2024,
+author={Sveinsson Cepero, Numi
+and Shadden, Shawn C.},
+title={SeqSeg: Learning Local Segments for Automatic Vascular Model Construction},
+journal={Annals of Biomedical Engineering},
+year={2024},
+month={Sep},
+day={18},
+issn={1573-9686},
+doi={10.1007/s10439-024-03611-z},
+url={https://doi.org/10.1007/s10439-024-03611-z},
+}
+```

seqseg-0.1.0/pyproject.toml

@@ -0,0 +1,51 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "seqseg"
+version = "0.1.0"
+description = "A simple deep learning-based medical image blood vessel tracking and segmentation tool."
+readme = "README.md"
+requires-python = ">=3.8"
+license = {text = "Apache-2.0"}
+authors = [
+    {name = "Numi Sveinsson Cepero", email = "numi@berkeley.com"},
+    {name = "Shadden Lab, UC Berkeley"}
+]
+keywords = [
+    "segmentation",
+    "deep learning",
+    "medical imaging",
+    "nnunet",
+    "medical image analysis",
+    "medical image segmentation",
+    "nnU-Net",
+    "blood vessel segmentation",
+    "vascular segmentation",
+    "vascular tracking"
+]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Medical Science Apps."
+]
+
+dependencies = [
+    "vtk",
+    "SimpleITK",
+    "PyYAML",
+    "nnunetv2",
+]
+
+[project.scripts]
+seqseg = "seqseg.seqseg:main"
+
+[project.urls]
+homepage = "https://github.com/numisveinsson/SeqSeg"
+repository = "https://github.com/numisveinsson/SeqSeg"
+
+[tool.setuptools]
+package-data = { "seqseg" = ["config/*.yaml"] }