CryoSPARC Guide
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Setup, Configuration and Management
Deployment Guides
Processing Data in cryoSPARC
Real-time processing in cryoSPARC Live
Cryo-EM Data Processing Explained
Topaz (Bepler, et al)
Overview of the Topaz wrapper available through cryoSPARC.
Introduction
The Topaz wrapper in cryoSPARC, introduced in v2.12, incorporates deep learning models used in Topaz to automatically pick particles with a set of previously-picked particles or to denoise micrographs. The wrapper consists of four jobs:
- Topaz Train
- Topaz Cross Validation
- Topaz Extract
- Topaz Denoise
Use the first three jobs for particle picking. Use final job for micrograph denoising.
Topaz is a particle detection tool created by Tristan Bepler, Alex J. Noble and team:
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Bepler, T., Morin, A., Rapp, M. et al. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat Methods 16, 1153–1160 (2019) doi:10.1038/s41592-019-0575-8
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Bepler, T., Noble, A.J., Berger, B. Topaz-Denoise: general deep denoising models for cryoEM. bioRxiv 838920 (2019) doi: <https://doi.org/10.1101/838920>
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Topaz License
Structura Biotechnology Inc. and cryoSPARC do not license Topaz nor distribute Topaz binaries. Please ensure you have your own copy of Topaz licensed and installed under the terms of its GNU General Public License v3.0.
Installing Topaz
cryoSPARC requires a Topaz installation in a dedicated Anaconda environment.
Create an Anaconda Python environment
Do not use the Anaconda Python installed with cryoSPARC. This installation is destroyed and recreated with cryoSPARC updates
Important considerations for Master/Worker or Cluster installations:
- The path to the Anaconda installation on the machine hosting
cryosparc_mastermust exactly match the path on machines hostingcryosparc_worker - The Anaconda installation directory must be accessible by the cryoSPARC Linux user account with the required permissions for executing the
topazbinary
Use a previously-installed Anaconda Python (3.6+), or install new one (Miniconda3 is also sufficient).
Create the
topaz Anaconda environment with the following commands:1conda create -n topaz python=3.62conda activate topaz # changes to the topaz conda environment3# Use `source activate topaz` with anaconda < 4.4 if properly configuredCopied!
Once created and activated, run the following command to install Topaz version 0.2.4:
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conda install topaz=0.2.4 cudatoolkit=11.2 -c tbepler -c pytorch -c conda-forge
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CryoSPARC has been tested with Topaz 0.2.4. Newer Topaz versions may also be compatible. More details on installing Topaz with Anaconda are available in the main Topaz repository: https://github.com/tbepler/topaz#installation
Find the Topaz Executable Path
Once Topaz is installed and the Anaconda environment is active in your current shell, enter the following command to determine the full path to the
topaz binary:1
which topaz
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The output should look similar to this:
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/home/cryosparcuser/anaconda3/envs/topaz/bin/topaz
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In the cryoSPARC interface, specify this as the value for the "Path to Topaz executable" parameter:
If using this path results in errors when running a Topaz job (often with a message such as "topaz did not produce valid output"), try aliasing Topaz with a shell script that also activates the correct Anaconda environment. This process is described in the next section.
(Optional) Create a topaz.sh wrapper script
CryoSPARC has its own Anaconda installation and environment which may conflict with the Topaz environment. To prevent this, create a shell script that deactivates the cryoSPARC environment and activates the topaz one.
Create a
topaz.sh file in a well known location such as the home directory (e.g., ~/topaz.sh). Add the following contents, making the noted substitutions:1
#!/usr/bin/env bash
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if command -v conda > /dev/null 2>&1; then
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conda deactivate > /dev/null 2>&1 || true # ignore any errors
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conda deactivate > /dev/null 2>&1 || true # ignore any errors
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fi
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unset _CE_CONDA
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unset CONDA_DEFAULT_ENV
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unset CONDA_EXE
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unset CONDA_PREFIX
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unset CONDA_PROMPT_MODIFIER
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unset CONDA_PYTHON_EXE
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unset CONDA_SHLVL
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unset PYTHONPATH
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unset LD_PRELOAD
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unset LD_LIBRARY_PATH
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source $HOME/anaconda3/etc/profile.d/conda.sh
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conda activate topaz
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exec topaz [email protected]
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- Substitute
$HOME/anaconda3on line 17 with the Anaconda installation directory.
Make this file executable by the cryoSPARC user from the command line
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chmod +x topaz.sh
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In the cryoSPARC interface, specify the full path to
topaz.sh as the "Path to Topaz executable" parameter: