NOVAS3D (Network of Vessel Analysis in 3D) is a CNN-based pipeline to extract vascular networks from 3D fluorescent microscopy images and track their morphological changes across time.
To install the current release run:
pip install novas3d
pip install git+https://github.com/Image-Py/sknw.git@18f18ab94794964a6dd7a76dd8a2c5c00dab6fd1For a tutorial on using the pipeline please see tutorial.ipynb
Ensure git-lfs is installed and enabled or else pickle files present in the example data and model files will not download properly.
git clone https://huggingface.co/datasets/mrozak/novas3d_example_data
git clone https://huggingface.co/mrozak/NOVAS3D_Vessel_and_Neuron_SegmentationIf you use NOVAS3D in your work please cite our paper:
Matthew Rozak James Mester Ahmadreza Attarpour Adrienne Dorr Shruti Patel Margaret Koletar Mary Hill JoAnne McLaurin Maged Goubran Bojana Stefanovic 2024 "A Deep Learning Pipeline for Mapping in situ Network-level Neurovascular Coupling in Multi-photon Fluorescence Microscopy" eLife13:RP95525 https://doi.org/10.7554/eLife.95525.2
For more details, see our docs.