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Job: Import Movies

Import raw movies.

Description

  • Import one or more raw movies for processing.

Input

  • Raw movies in .mrc, .mrc.bz2 , .tif or .eer formats.
For .eer file support, please see:
If working with negative stain or phase plate data, please see:

Common Parameters

  • Movies data path: Click on the folder icon to browse or paste the path specifying the location where the movies are stored. To select multiple files, enter a wildcard expression in the browse bar, e.g., *.mrc, which will select all matching file types in the subfolder.
  • Gain reference path: Specify the path to the gain reference file, if available.
  • 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 dark background (-1). If it's off, this indicates the movies have dark particles on 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.

XML Beam Shift Import Parameters

For additional information on importing movies with XML files, refer to the EPU AFIS Beam Shift Tutorial.
  • EPU XML metadata path: Absolute path, wildcard-expression (e.g. /mount/data/somewhere/*.xml) for importing EPU XML files with beam shift. Only .xml files are supported
  • Length of movie filename prefix to cut for XML correspondence: Use this field to specify the number of characters to cut off the prefix of the imported movie filename, to match with the XML filename.
  • Length of movie filename suffix to cut for XML correspondence: Use this field to specify the number of characters to cut off the suffix of the imported movie filename, to match with the XML filename.
  • Length of XML filename prefix to cut for movie correspondence: Use this field to specify the number of characters to cut off the prefix of the XML filename, to match with the imported movie filename.
  • Length of XML filename suffix to cut for movie correspondence: Use this field to specify the number of characters to cut off the suffix of the XML filename, to match with the imported movie filename.

Movie Correspondence Parameters

These parameters are only used if input movies are connected to the job's inputs, and correspondences must be made between the input (connected) movies and the imported movies found by the job. This is a feature added to address a corner-case where beam shift metadata must be imported and assimilated into an existing movie dataset in CryoSPARC; for more information, refer to the EPU AFIS Beam Shift Tutorial.
This feature, and the associated parameters below, function similarly to those described in Import Micrographs: Linking Micrographs to Input Movies.
  • Length of input movie path prefix to cut: Use this field to specify the number of characters to cut off the prefix of the input movie filename, to match with the imported dataset's filename.
  • Length of input movie path suffix to cut: Use this field to specify the number of characters to cut off the suffix of the input movie filename, to match with the imported dataset's filename.
  • Length of imported movie path prefix to cut: Use this field to specify the number of characters to cut off the prefix of the imported movie filename, to match with the input dataset's filename.
  • Length of imported movie path suffix to cut: Use this field to specify the number of characters to cut off the suffix of the imported movie filename, to match with the input dataset's filename.

Output

  • Imported movies (which can be used in other CryoSPARC jobs)

Common Next Steps

  • Full frame motion correction to generate micrographs from which particles can be picked manually or using template-based automatic picking