Algorithms for Single Particle Reconstruction
ASPIRE - Algorithms for Single Particle Reconstruction - v0.6.3
This is the Python version to supersede the Matlab ASPIRE.
ASPIRE is an open-source software package for processing single-particle cryo-EM data to determine three-dimensional structures of biological macromolecules. The package includes advanced algorithms based on rigorous mathematics and recent developments in statistics and machine learning. It provides unique and improved solutions to important computational challenges of the cryo-EM processing pipeline, including 3-D ab-initio modeling, 2-D class averaging, automatic particle picking, and 3-D heterogeneity analysis.
For more information about the project, algorithms, and related publications please refer to the ASPIRE Project website.
For full documentation see the docs.
ASPIRE is a pip-installable package that works on Linux/Mac/Windows, and requires Python 3.6. The simplest option is to use Anaconda 64-bit for your platform with a minimum of Python 3.6 and
pip, and then use
pip to install
aspire in that environment.
conda create -n aspire_env python=3.6 pip conda activate aspire_env pip install aspire
The final step above should install any dependent packages from
pip automatically. To see what packages are required, browse
Note that this step installs the base
aspire package for you to work with, but not the unit tests/documentation. If you need to install ASPIRE for development purposes, read on.
After cloning this repo, the simplest option is to use Anaconda 64-bit for your platform, and use the provided
environment.yml file to build a Conda environment to run ASPIRE. This is very similar to above except you will be based off of your local checkout, and you are free to rename
aspire_dev used in the commands below. The
pip line will install aspire in a locally editable mode, and is equivalent to
python setup.py develop:
cd /path/to/git/clone/folder # Create's the conda environment and installs base dependencies. conda env create -f environment.yml --name aspire_dev # Enable the environment conda activate aspire_dev # Install the aspire package in a locally editable way: pip install -e .
If you prefer not to use Anaconda, or want to manage environments yourself, you should be able to use
pip with Python >= 3.6.
Please see the full documentation for details.
You may optionally install additional packages:
# Additional GPU packages (reqires CUDA) pip install -e ".[gpu]" # Additional developer tools pip install -e ".[dev]"
Make sure everything works
Once ASPIRE is installed, make sure the unit tests run correctly on your platform by doing:
cd /path/to/git/clone/folder pytest
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
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