Job: Topaz Extract
Topaz Extract job available via wrapper in CryoSPARC.
Topaz Trainjob has been used to train a Topaz model it can be used to pick particles from micrographs using the
Topaz Extractjob. This job has the following inputs and outputs:
- Topaz Model
- Particle Picks
Topaz Extractjob 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 Extractjob 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 Picksjob 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.
The particle picks from the
Topaz Extractjob can be observed and have a threshold applied using the Inspect Particle Picks job. This job interacts with particle picks from
Topaz Extractdifferently 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 Picksjob. 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.
Sample Topaz Extract Results with T20S Proteasome
All particles outputted from
Topaz Extractmust be processed using the
Extract from Micrographsjob in CryoSPARC. This updates the CTF information within the particle picks and makes the picks compatible with other CryoSPARC jobs such as