Detects sub-precision contacts between subcellular organelles in 2 and 3D STED (precision ~ 50-150nm) superresolution microscopy, for example endoplasmum reticulum and mitochondria (contacts ~ 20-100nm).

Where a pixel precise segmentation is not feasible due to the precision of the microscope, and colocalization does not describe the interface in a meaningful way, SubPrecisionContactDetection can reconstruct the plausible interface between the organelles.

An example rendering of the postprocessed contact zones (white) between endoplasmum reticulum (green) and mitochondria (red) is shown here (source):

• Fast: using multiple threads, and Julia's fast LLVM JIT code
• Reproducible: tests ensure backwards compatibility
• Configurable: Can process deconvolved or raw images, with optional extra denoising
• Rich: provides interpretable features for each detected contact
• Confidence map for each voxel (each voxel has a p-value)

If you find this project useful, please cite

@article{cardoen2023membrane,
  title={Membrane contact site detection (MCS-DETECT) reveals dual control of rough mitochondria--ER contacts},
  author={Cardoen, Ben and Vandevoorde, Kurt R and Gao, Guang and Ortiz-Silva, Milene and Alan, Parsa and Liu, William and Tiliakou, Ellie and Vogl, A Wayne and Hamarneh, Ghassan and Nabi, Ivan R},
  journal={Journal of Cell Biology},
  volume={223},
  number={1},
  pages={e202206109},
  year={2023},
  publisher={Rockefeller University Press}
}