Job: Reassign Particles to Micrographs

Link particles back to the micrographs they came from.


The Reassign Particles to Micrographs job can be used to link particles back to the micrographs they came from by matching their file names.


  • micrograph dataset

  • particle dataset

    • location result field


  • micrograph dataset (passthrough)

  • particle dataset (linked to micrograph dataset)

Common Next Steps

  • Particle extraction via Extract From Micrographs

Example Use Case

Consider a scenario where you receive pre-aligned micrographs from a microscope facility and start processing them in CryoSPARC. After you obtain your final subset of particles, you want to improve the resolution of your structure by aligning the raw movies in CryoSPARC using Patch Motion Correction. The problem is when you imported your movies, CryoSPARC created a new unique dataset for them, so connecting the new micrographs and the particles from the pre-aligned micrographs to the "Extract From Micrographs" job doesn't work, as there is no association between these datasets. In this case, you can use the "Reassign Particles to Micrographs" job. CryoSPARC uses the filename of a movie to create the filename of its micrograph, which is then used to create the filename of its particle stack. You can re-associate a particle dataset back to a micrograph dataset using the common part of the path, which this job helps you do.

The usage of this job is similar to the Import Particles and Import Micrographs job. When you run the Reassign Particles to Micrographs 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 filename and/or the source filename such that the query matches the source.

Consider the following case:

Loaded particle stack with 8474 items

Loaded 20 micrographs

Example source micrograph 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, 002748358406320475195_ from the prefix of the query, .frames_patch_aligned.mrc from the suffix of the query, and .frames_patch_aligned_doseweighted.mrc from the suffix of the source. You can use a site like to count the number of characters. The parameters for the job should therefore be:

Length of input micrograph path suffix to cut : 38
Length of location/micrograph_path prefix to cut for query : 22
Length of location/micrograph_path path suffix to cut for query : 25

You can now take the outputs of this job, and connect them to an "Extract From Micrographs" job, or any other job that requires particles and micrographs.

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