Cell Curvature Analysis
Cell curvature is an important morphological feature of cell shape and involved in organizing cell signaling (e.g. through Septin localization).
To measure and visualize cell curvature (Manuscript Figure 3), we developed custom Matlab code that takes a binary cell segmentation mask, measures the curvature, and generates a collada (.dae) file for visualization. The collada file format can be easily imported (opened) in ChimeraX: https://www.cgl.ucsf.edu/chimera/.
Matlab code
If you run the Matlab code, first clone this Github repository and set Matlab’s path to
include all the Matlab functions provided by
the Highres_curvature package on the GitHub repository,
using the Set Path
button in Matlab (Home > Environment > Set Path> Add with subfolders).
To run the cell curvature analysis of a cell, open runMeasureCurvature.m by typing
“edit runMeasureCurvature” in Matlab’s command window. runMeasureCurvature.m is the main
script to extract the cell curvature and generate a Collada file for visualization.
In this script, revise the “imageDirectory” for loading the data and “saveDirectory”
for saving the results. Save the changes and run the function by typing “runMeasureCurvature”
in Matlab’s command window.
Matlab compiled version
If you do not have access to Matlab, we provide a compiled version of the code as “.exe” file. To run it, please double click on the compiled version and follow the installation instructions. In the installation process also a Matlab runtime environment is installed to run the code (if not already available). After installation, the compile code is ready to run. For this, click on MatlabCompiler_measureCurvature.exe to run the code and follow the prompts to select a .tif file.
Output:
The Matlab file generates an Excel file with all the vertices of the surface mesh (meshSurface.xlsx), an Excel file with the mean and Gaussian curvature values (Curvature.xlsx) and the collada file for rendering in Chimera (see image below).
.
|-- curvaturefolder
| |-- curvatureExample.tif
| | Results
| | | |--meshSurface.xlsx
| | | |--Curvature.xlsx
| | | |--curvatureExample_curvature.dae
Test data for cell curvature analysis
Test data is available for the cell shape feature analysis in the folder Code_Example_Datasets/Exemplary_CurvatureAnalysis:
- on Synapse:
- or Zenodo:
It contains a segmented cells to visualize.