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Cryo-EM Heterogeniety Challenge

This repository contains the code used to analyse the submissions for the Inaugural Flatiron Cryo-EM Heterogeneity Challenge.

Scope

This repository explains how to preprocess a submission (80 maps and corresponding probability distribution), and analyze it. Challenge participants can benchmark their submissions locally against the ground truth and other submissions that are available on the cloud via the Open Science Foundation project The Inaugural Flatiron Institute Cryo-EM Heterogeneity Community Challenge.

Warning

This is a work in progress, while the code will probably not change, we are still writting better tutorials, documentation, and other ideas for analyzing the data. We are also in the process of making it easier for other people to contribute with their own metrics and methods. We are also in the process of distributiing the code to PyPi

Accessing the data

The data is available via the Open Science Foundation project The Inaugural Flatiron Institute Cryo-EM Heterogeneity Community Challenge. You can download via a web browser, or programatically with wget as per this script.

Installation

Installing this repository is simply. We recommend creating a virtual environment (using conda or pyenv), since we have dependencies such as PyTorch or Aspire, which are better dealt with in an isolated environment. After creating your environment, make sure to activate it and run

cd /path/to/Cryo-EM-Heterogeneity-Challenge-1
pip install .

Running

If you want to run our code, please check the notebooks in the tutorials folder.

The tutorials explain how to setup the config files, and run the commands

cryo_challenge run_preprocessing                      --config config_files/config_preproc.yaml
cryo_challenge run_svd                                --config config_files/config_svd.yaml
cryo_challenge run_map2map_pipeline                   --config config_files/config_map_to_map.yaml
cryo_challenge run_distribution2distribution_pipeline --config config_files/config_distribution_to_distribution.yaml

Acknowledgements

  • Miro A. Astore, Geoffrey Woollard, David Silva-Sánchez, Wenda Zhao, Khanh Dao Duc, Nikolaus Grigorieff, Pilar Cossio, and Sonya M. Hanson. "The Inaugural Flatiron Institute Cryo-EM Heterogeneity Community Challenge". 9 June 2023. DOI:10.17605/OSF.IO/8H6FZ
  • David Herreros for testing and CI and debugging in this repo

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