SMT_Unwrapping

SMT_unwrapping contains the Matlab scripts for single-molecule tracking in bacteria cells considering the curvature of the cell envelope.

• TrackingMainscript links single particals/molecules/spots from 2D or 3D result with correct format using nearest neighbour algorithm.
  • it also filters bad spots or trajectories by user defined intensity threshold and ROI based on bright field or fluorescence image
• UnwrappingMainscript helps rotate individual cells and unwrap the cell envelope (it only applys to the rod shape cells now).
• State_Segementation helps segment indivudual reajectoies to different states (it only distinguishs directional movement from confined diffusion ones now).
• FtsW2dPostprocess does simple statistics of the results with some plotting functions.

Request

1. Require Matlab 2020a or newer for some functions in the GUI.
2. Molecules are identified and localized using imageJ plugin ThunderSTROM:.
3. Bright field (or PhaseContrast) images of bacteria cells are required for estimation of the cell diameter.

How to use

1. To process data from 2d single-molecule tracking, please find the step-by-step manual in HowToUse2dTracking.
2. To process data from 2d single-molecule tracking in nanopilars, please find the the step-by-step manual in Alink.
3. To process data from 3d single-molecule tracking, please find the the step-by-step manual in Alink.

Reference

Please cite this paper Yang, Xinxing, et al. "A two-track model for the spatiotemporal coordination of bacterial septal cell wall synthesis revealed by single-molecule imaging of FtsW." Nature Microbiology (2021): 1-10.