RELION-format stack handling

We currently offer RELION software for analyzing single particle cryo-EM data.

Guidelines for uploading data in RELION format

Short version:

Upload your entire Extract directory into COSMIC² from RELION using Globus. All files found will be displayed in the data listing page when upload completes.

Long version:

  • COSMIC² expects either of the following input data structures:
    1. Uploaded directory has RELION extracted particles with STAR file within uploaded directory named
    2. Uploaded directory has subdirectories, where each subdirectory has a STAR file named 
      • Each subdirectory will be listed as a separate dataset
  • For RELION2 and RELION3 users, this means you just have to upload Extract directory and then every sub-directory (job001, job002, etc) will be listed as separate datasets


  • Uploaded directory name: Extract
    • With subdirectories: Extract/job001, Extract/job002
  • Location of file: Extract/job001/particles.starExtract/job002/
  • Location of extracted particle images (anywhere within subdirectory: Extract/job001/Micrographs, Extract/job002/Micrographs/
  • Example particle entry line from Extract/job001/Micrographs/file001.mrcs  
  • Will be displayed as the following on COSMIC²:Extract/job001/particles.starExtract/job002/

Uploading cryoSPARC-extracted particle stacks

You can upload cryoSPARC stacks as long as you convert the .cs files to .star format. Learn more here.