Job: Topaz Extract

Topaz Extract job available via wrapper in CryoSPARC.

Once the Topaz Train job has been used to train a Topaz model it can be used to pick particles from micrographs using the Topaz Extract job. This job has the following inputs and outputs:


  • Topaz Model

  • Micrographs


  • Particle Picks

  • Micrographs


The Topaz Extract job features various parameters but the most notable parameter is the particle threshold parameter. This parameter determines the minimum quality threshold at which to accept particle picks. If the results of a Topaz Extract job features too many particles, the issue may be solved simply by increasing this parameter. However, selecting an improved threshold can be conveniently done using the Inspect Particle Picks job in cryoSPARC as detailed in the next section.

This job also features the number of parallel threads parameter. Like in the Topaz Train and Cross Validation jobs, this parameter decreases the preprocessing time by a factor approximatly equal to the input value. It is recommended to set this value to at least 4 as the preprocessing time is often a bottleneck in time performance of the job. Values less than 2 will default to single thread.

Interpreting Training Results from Topaz Extract

The particle picks from the Topaz Extract job can be observed and have a threshold applied using the Inspect Particle Picks job. This job interacts with particle picks from Topaz Extract differently in that it enable a user to apply a threshold based on Topaz model performance rather than power score. To do so, vary the power score threshold in the Inspect Particle Picks job. In the image below, the inferred picks have a lower bound threshold of 15 and an upper bound threshold of 48 applied. This number is a model score applied by Topaz indicating how confident the model is in a particle pick.

All particles outputted from Topaz Extract must be processed using the Extract from Micrographs job in CryoSPARC. This updates the CTF information within the particle picks and makes the picks compatible with other CryoSPARC jobs such as Ab-Initio Reconstruction.

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