ODT-SAS is a new semi-automatic method that uses conventional approaches (not based on machine learning) to process optical diffraction tomography (ODT) images of biological cells. It enables 3D segmentation of whole biological cells and 2 types of their organelles: nucleolus and lipid structures.
Base Requirements
- Matlab R2020b or later
- Graphic card that utilizes CUDA technology, with a Compute Capability >= 2.0
- Installed CUDA driver
Other Requirements
- ASTRA Toolbox (Version 1.8 or later: MATLAB toolbox)
- Spot: A Linear-Operator Toolbox (Version 1.2 or later: Spot Toolbox)
- Download the repository
- Download MATLAB Toolboxes indicated in the requirements and move them to the "ASTRA Tool" folder
- Run ODT_SAS.m file
Before running ODT_SAS.m, please read Code instruction
If you find the work useful, please cite the following paper:
M. Mazur and W. Krauze, "Volumetric segmentation of biological cells and subcellular structures for optical diffraction tomography images", Biomed. Opt. Express 14, 5022-5035 (2023).