# Job: Patch CTF Extraction

## At a Glance

<figure><img src="/files/P31ZaakmYZNMjadTNEMm" alt="A flowchart. We start with micrographs without CTF estimates. Particle images are picked from these micrographs, and the micrographs are separately run through Patch CTF Estimation. Patch CTF Extraction is used to produce particle images with CTF estimates."><figcaption></figcaption></figure>

Apply CTF estimates from micrographs to particle locations which were picked or extracted before CTF estimation.

## Description

If particles are picked before CTF estimation is performed, those particles will not have CTF estimates and cannot be used in downstream analyses. Rather than re-pick or re-extract particles from micrographs with CTF estimates, Patch CTF Extraction allows particle CTF estimates to be updated directly.

In a typical workflow particles are picked after a [Patch CTF](/processing-data/all-job-types-in-cryosparc/ctf-estimation/job-patch-ctf-estimation.md) job. In that case this job is unnecessary, since the particles would have CTF estimates from their extraction job.

## Inputs

### Micrographs

This job requires micrographs with CTF estimates, typically from a [Patch CTF](/processing-data/all-job-types-in-cryosparc/ctf-estimation/job-patch-ctf-extraction.md) job.

### Particles

This job accepts either particle picks or extracted particle images. If picks are provided, they will have to be [extracted](/processing-data/all-job-types-in-cryosparc/extraction/job-extract-from-micrographs.md) before downstream use.

## Commonly Adjusted Parameters

### Flip mic. in x/y before extract

If particles were picked in external software, the coordinates may need to be flipped using one or both of these parameters before extraction. If CryoSPARC was used to pick particles, both of these parameters should be left off.

## Outputs

### Particles

If extracted particle images were provided as an input, the output particle images have a CTF and are ready for further use. If particle pick locations were provided, these particles need to be [extracted](/processing-data/all-job-types-in-cryosparc/extraction/job-extract-from-micrographs.md) before use.

## Recommended Alternatives

If providing particle pick locations (i.e., not extracted particles), it may be more convenient to use the Force re-extract CTFs from micrographs parameter of [Extract From Micrographs](/processing-data/all-job-types-in-cryosparc/extraction/job-extract-from-micrographs.md) rather than this job. This combines the CTF update and image extraction steps into a single job.


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