MemBrain-stats is a Python project developed by the CellArchLab for computing membrane protein statistics in 3D for cryo-electron tomography (cryo-ET).
As a first step, you need to prepare the data. The most important ingredients for MemBrain-stats are protein locations and membrane meshes. More information on how to prepare the data can be found here.
All functionalities can be accessed via the command line interface (CLI). To get an overview of all functionalities, run:
membrain_statsThe command protein_concentration computes the number of proteins per membrane area. It can be accessed via the command line interface (CLI) by running:
membrain_stats protein_concentration --in-folder <path/to/folder>More information can be found here.
The command geodesic_NN computes the geometric distances between nearest neighbors in the membrane. It can be accessed via the command line interface (CLI) by running:
membrain_stats geodesic_NN --in-folder <path/to/folder> --start-classes <list_of_classes> --target-classes <list_of_classes>More information can be found here.
The command geodesic_ripley computes Ripley's statistics for all membrane meshes in a folder. It can be accessed via the command line interface (CLI) by running:
membrain_stats geodesic_ripley --in-folder <path/to/folder> --start-classes <list_of_classes> --target-classes <list_of_classes>More information can be found here.
The edge exclusion functionality can be used to exclude the edges of the membrane from the analysis. It can be accessed as an optional argument to many of the functionalities. More information can be found here.
MemBrain-stats can merge outputs from the Surface Morphometrics Pipeline into the membrane containers produced by MemBrain-pick. This enables the joint analysis of particle positions with respect to different properties computed by the pipeline, like curvature or inter-membrane distance. More information can be found here.