# Job: Topaz Extract

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:

**Inputs**

* Topaz Model
* Micrographs

**Outputs**

* Particle Picks
* Micrographs

## Parameters

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.

![Sample Topaz Extract Results with T20S Proteasome](https://1916621962-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-M7DGv3GkRvGGpbVPCgg%2F-M9yAexncOkUt6ZRF5cD%2F-M9yB0ibs0Ms0WRQm0H9%2Ftopaz_inf.png?alt=media\&token=9f7a391d-a89a-4222-9e32-8f989d38b33b)

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`.