This Guide contains detailed information on installing, configuring and using cryoSPARC v0.2.47 to 0.6.5. For detailed documentation, installation instructions and a tutorial for cryoSPARC v2.0+, please visit our new documentation page at We highly recommend upgrading to v2.0 to take advantage of the full pipeline for processing single particle cryo-EM data, as well as powerful new workflow features.


The Datasets page displays all datasets opened in cryoSPARC in reverse chronological order, along with a random selection of particle images from each. Click on a dataset to view its details. Users can toggle between Card and List view.


Create a new dataset

  1. From the Datasets page, click ‘New Dataset’.
  2. On the left-hand sidebar, click ‘Configure’.
  3. Click ‘Add New File Set’ and select particle stack files and meta data files as required.

Working with .star files:

  • The .star file references multiple .mrc stacks
    • If the paths in the .star file are relative to the .star file’s location, then leave the ‘Image Data File’ path blank
    • If not, the Image Data File must be a directory that contains the .mrc stacks (it’s okay if they are in sub-folders; cryoSPARC will find them)
  • The .star file references a single .mrc stack
    • If the paths in the .star file are correct, ‘Image Data File’ can be left blank
    • If you want to use a different stack than the one pointed to in the .star file, give the path in ‘Image Data File’ and this will override the .star file

Working with .txt, .par, or .emx files:

  • For Image Data File, provide the path to a single .mrc stack that contains all the particles in the same order as the Meta Data File



Microscope parameters

By default, all of the microscope parameters are empty and will be drawn from the Meta Data File. Descriptions for each parameter are found to the right of each value.

Changing a parameter manually overrides the corresponding value in the Meta Data File. To change a parameter manually, type the chosen value into the field. To reset to default, click on the “x” next to a given parameter value.

Visualize and load dataset

After creating a new dataset and changing microscope parameters as desired, click on the ‘Visualize’ tab on the left. Click ‘Launch’ to have cryoSPARC load and display the data to verify the integrity of the files provided and the correctness of the microscope parameters.