A rapid surface extraction algorithm in Python for 3D microscopy datasets.
mSME is able to extract a comprehensive and continuous surface from the 3D volume, with improvements in performance, speed, and usability than the original FastSME algorithm: Basu et al.
Full methods described in: G. Gao et al. “Comprehensive surface histology of fresh resection margins with rapid open-top light-sheet (OTLS) microscopy.” IEEE Trans. Biomed. Eng.
Please cite our paper if you find this package useful.
In order to use mSME's GPU acceleration, install CUDA Toolkit.
Clone this repository:
git clone https://github.com/alecgao066/mSME.git
cd mSMEInstall all dependencies at a new conda environment (surface_extraction):
conda env create -f environment.ymlSee example.ipynb to get started.
Example image stack provided via shared google drive link.
Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.