membrain-pick 0.0.7

membrane protein localization for cryo-ET

Membrain-Pick

Overview

Membrain-Pick is part of the MemBrain suite of tools for processing membranes in cryo-electron tomography. MemBrain-pick's main purpose is to localize membrane-associated particles in the tomograms. To this end, MemBrain-picks takes as input already existing membrane segmentations and processes these to limit the search space for membrane-associated particles. The output of MemBrain-pick is a set of coordinates that can be used for further analysis.

Workflow

The workflow of MemBrain-pick is as follows:

1. Input: Membrane segmentations in the form of a binary mask (.mrc). Ideally, these segmentations should depict single membrane instances.
2. Mesh Generation: The membrane segmentations are converted into a mesh representation. At this stage, also tomogram densities are projected onto the membrane mesh.
3. Ground Truth Generation: The membrane mesh can be loaded into surforama to manually annotate membrane-associated particles. These annotations can then be used to train a MemBrain-pick model.
4. Training: The generated meshes, along with the annotations, are used to train a model that can predict the location of membrane-associated particles.
5. Prediction: The trained model is used to predict the location of membrane-associated particles in the membrane segmentations.

Example notebook

For a quick start, you can walk through our example notebook. You can easily run it on Google Colab by clicking on the badge below:

Key Functionalities

• Mesh Conversion: Transform membrane segmentations into a mesh representation that can easily be processed by MemBrain-pick and surforama.
• Model training: Train a model to predict the location of membrane-associated particles.
• Prediction: Use the trained model to predict the location of membrane-associated particles in membrane segmentations.
• Initial orientaton assignment: Given a set of positions, MemBrain-pick can assign initial orientations to the particles by aligning them with the membrane normal. -- integration with surforama: MemBrain-pick can be used in conjunction with surforama to manually annotate membrane-associated particles.

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Jump to

• Installation
• Data Preparation
• Training
• Prediction
• Angle Assignment
• Visualization in Surforama

MemBrain-pick is part of the MemBrain v2 [1] package and still under early development. If you have any questions or suggestions, please contact us at [e-mail]

[1] 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., and Peng, T, 2024. MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography. bioRxiv, https://doi.org/10.1101/2024.01.05.574336