CryoSPARC Guide

Job: Import Micrographs

Import motion-corrected micrographs (exposures).


The Import Micrographs job allows you to import one or more micrographs into CryoSPARC for processing. You can optionally link these micrographs to their corresponding movies by connecting the movies as an input to this job.


  • .mrc file(s)

Common Parameters

  • It is best to specify the Raw pixel size (A), Accelerating voltage (kV), Spherical aberration (mm) and Total exposure dose (e/A^2) if known
  • Negative Stain Data: If Negative Stain Data is on, this indicates that there are light particles on a dark background (-1). If it's off, this indicates the movies have dark particles on a light background (cryo-em data, +1).
  • Phase Plate Data: Indicates if data was collected using a phase plate.
  • Skip Header Check: Enabled by default in v4.2+, disables the reading of each exposure file's header to ensure that all movies are of the same size (resolution). If disabled, use the "Number of CPUs to parallelize during header check" parameter to parallelize reading of exposure headers.


  • Imported micrographs

Common Next Steps

  • Particle picking

Linking Micrographs to Input Movies

In the scenario where you want to link your micrographs to a movie dataset that is already in CryoSPARC, you can connect the movies to the inputs of this job.
Similar to Import Particles and Reassign Particles to Micrographs, in order to match the imported micrographs with the input movies, you need to use the parameters of the job to tune the query filename that will be used to link the files.
When you run the job, you'll see an example of the source filename and an example of the query filename. The objective is to cut enough characters from both the query and/or source filename such that they match each other.
Consider the following case:
Importing 20 files
Attempting to find corresponding filenames in imported micrographs and connected input movies..
Example source movie filename:
Example query micrograph filename:
In order to match the query with the source, we're going to have to cut characters from both strings. Specifically, 005037141451040249225_ from the prefix of the source, .frames.tif from the suffix of the source, 000540129543984053453_ from the prefix of the query, and .frames_patch_aligned_doseweighted.mrc from the suffix of the query. You can use a site like to count the number of characters. The parameters for the job should therefore be:
Length of movie path prefix to cut : 22
Length of movie path suffix to cut : 11
Length of mic. path prefix to cut : 22
Length of mic. path suffix to cut : 38
Now, the imported micrographs will be linked to the movies already in CryoSPARC, allowing you to come back to preprocessing steps easily.

Example Workflow (Micrographs)