Topaz is a software package for particle detection and image denoising in cryo-electron microscopy (cryo-EM) that uses convolutional neural networks.
Availability and Restrictions
Versions
Topaz is available on the OSC clusters. The versions currently available at OSC are:
| Version | Pitzer | Ascend | Cardinal |
|---|---|---|---|
| 0.3.20 | X | X | X |
You can use module spider topazto view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.
Access
Topaz is available to all OSC users.
Publisher/Vendor/Repository and License Type
Open Source (GPL-3.0)
Bepler, T., Morin, A., Rapp, M., Brasch, J., Shapiro, L., Noble, A.J.*, Berger, B.* (2019). Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nature Methods. https://doi.org/10.1038/s41592-019-0575-8
Usage
Set Up
Load the topaz module with module load topaz/<version>. For example, run module load topaz/0.3.20 to load version 0.3.20. In order to run Topaz, you will need to request a GPU. In your job script, include:
#SBATCH --gpus-per-node=1
For more information, see GPU Computing.
Run Topaz Commands
To run a Topaz command, use topaz <command> [options]. For example:
topaz preprocess -v -s 8 -o data/EMPIAR-10025/processed/micrographs/ data/EMPIAR-10025/rawdata/micrographs/*.mrc
