scipion-em / scipion-em-membrain

Plugin to run MemBrain software within Scipion

Membrain plugin for Scipion

This plugin implements protocols from the MemBrain family of software packages for analysis of membrane proteins in cryo-electron tomography.

Installation

The plugin is currently only available in development mode. To install, proceed with the following steps:

Clone this repo:

git clone https://github.com/scipion-em/scipion-em-membrain.git

Install this plugin in devel (editable) mode:

scipion3 installp -p /path/to/scipion-em-membrain --devel

Scipion will automatically install MemBrain and download any pre-trained models necessary for running it.

Configuration variables

There are some optional variables related to the MemBrain installation. For example, if you have installed MemBrain-seg outside of Scipion, you may define MEMBRAIN_SEG_ENV_ACTIVATION in your scipion.conf file for specifying an already existing conda environment or a script to be sourced:

MEMBRAIN_SEG_ENV_ACTIVATION = conda activate my-membrain-seg-env

Also, you can use the MEMBRAIN_SEG_MODEL environment variable to indicate the full path to a MemBrain-seg model downloaded externally:

MEMBRAIN_SEG_MODEL = /path/to/membrain-seg/model.ckpt

If these variables are not defined, default values will be used that will work with the latest version installed through Scipion.

Protocols

The following protocols are currently implemented:

• Membrane segmentation using the MemBrain-seg module

Using GPU or CPU

By default, MemBrain protocols assume that a GPU card is available. If such a device is not found, protocols may still run using the CPU with parallel threads, but will be much slower.

References

<!-- in JSB citation style: -->

• Lamm, L., Zufferey, S., Righetto, R.D., Wietrzynski, W., Yamauchi, K.A., Burt, A., Liu, Y., Zhang, H., Martinez-Sanchez, A., Ziegler, S., Isensee, F., Schnabel, J.A., Engel, B.D., Peng, T., 2024. MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography. https://doi.org/10.1101/2024.01.05.574336
• Lamm, L., Righetto, R.D., Wietrzynski, W., Pöge, M., Martinez-Sanchez, A., Peng, T., Engel, B.D., 2022. MemBrain: A deep learning-aided pipeline for detection of membrane proteins in Cryo-electron tomograms. Computer Methods and Programs in Biomedicine 224, 106990. https://doi.org/10.1016/j.cmpb.2022.106990

Contact information

If you experiment any problem, please contact us here: [e-mail] or open an issue.

We'll be pleased to help.

Scipion Team