> For the complete documentation index, see [llms.txt](https://guide.cryosparc.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/deep-picking/topaz/job-topaz-extract-beta.md). # 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](/files/-M7DHN16x9YcaQnDlRxh) 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`. --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/deep-picking/topaz/job-topaz-extract-beta.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.