Job: Volume Tools

Apply various operations including upsample, downsample, crop, pad, flip, etc., to a volume or mask.


Use this job to one or more of the following operations on an input Volume or Mask:

  • Upsample/Downsample

  • Crop

  • Add soft padding

  • Flip handedness

  • Lowpass filter

  • Invert density (subtract input from ones)

    • Note that both volumes and masks can be inverted. As of CryoSPARC v4.4, if inversion is activated, it will take place after any thresholding, dilation, or padding (if used).

In addition, masks can be generated from thresholded input volumes or masks. Mask generation has the following operations:

  • Dilation

  • Applying a soft padding

  • Clip a mask along the z-axis (for helical refinements)


  • A map volume or mask

Common Parameters

Note: Volume operations are done in the following order:

  1. Resampling, lowpass filtering, and cropping

  2. Thresholding, dilation, and padding (if enabled)

  3. Inversion (if enabled)

  • Type of input volume: Choose whether to use the volume or mask input slot. The volume operations are only applied to the input at the selected slot

  • Type of output volume: The type of the output once the Volume Tools operations are complete. Can be the same or different from the type of the input volume

  • Lowpass filter (A): Lowpass filter the input volume to this resolution in Angstroms, prior to additional processing.

For Mask Generation

  • Threshold: This is the threshold value that is used to binarize the input density map, to convert it into a mask. See callout above about the order of operations applied to the volume.

    • Note: To generate a mask from a volume that has been lowpass filtered, run an initial Volume Tools job to lowpass filter the volume, then view the density in the volume viewer (or download and view in UCSF Chimera) to choose a threshold value, and run a second job with the threshold set.

  • Dilation radius (pix): The radius of the spherical mask used to dilate the mask, in units of pixels of the final resampled volume. Leave as 0 to skip dilation.

  • Soft padding width (pix): The width of the cosine-padded region at the edge of the mask, in units of pixels of the final resampled volume. Setting to 0 will skip soft padding. Note: the soft padding should never be skipped if the mask is to be used for any downstream jobs in CryoSPARC, since softly-padded masks are required by all jobs that use masks!


  • The edited input map volume or mask

Common Next Steps

Last updated