This software was developed to analyze the membrane-bound ribosome density and curvature of ER membranes in cryo-electron tomograms.
This folder contains MATLAB scripts used to map ribosome center coordinates obtained by template matching onto a membrane mask from tomogram segmentation. Usage details can be found in the README file inside this folder.
Please note that TOM MATLAB package (Hrabe et al., 2012; http://www.biochem.mpg.de/tom) is required for reading and writing EM and MRC files and generating a mask from a motive list. MATLAB/2015b version was used to run these scripts.
This folder contains Python packages with scripts used for the following two analyses:
-
Calculation of ribosome density on ER membranes using a mask with ribosome coordinates on a membrane (obtained using the scripts in 'ribosome_centers_mapping' folder) and the membrane mask. An example execution code for this task can be found in the 'main' method in 'ribosome_density/ribosome_density.py'.
-
Estimation of membrane curvature using our implementation of Normal Vector Voting algorithm (Page et al., 2002). The workflow consists of the following three main steps: 1. signed surface generation, 2. surface cleaning using a graph, and 3. curvature calculation using a graph generated from the clean surface. The function 'workflow' in 'curvature/tomogram_batch_processing.py' provides the complete execution code, which can be called as shown in the 'main' function.
Please note that the following Python packages are required and have to be installed:
- Pyto ImageIO (Lučić et al., 2016, PMID: 27742578 DOI: 10.1016/j.jsb.2016.10.004)
- VTK (http://www.vtk.org)
- graph-tool (Peixoto, 2014; https://git.skewed.de/count0/graph-tool)
The scripts can be run using Python 2.7 versions.