Job: Split Volumes Group

At a Glance

Split a volumes group into several individual volume outputs, optionally splitting particles as well.

Description

Split Volumes Group Job

The Split Volumes Group job type allows for converting a volumes group into a number of individual volume outputs. This is useful if specific volumes from within a volumes group need to be manually selected or connected to downstream jobs. A set of particles corresponding to the volumes group can also be connected as input to the job, and those particles will be split according to their classification amongst the volumes in the group.

Volumes groups

Volumes groups are new in CryoSPARC v4.5+.

In CryoSPARC, jobs such as Ab-Initio Reconstruction, Heterogeneous Refinement, 3D Classification, Regroup 3D Classes, Heterogeneous Reconstruct Only, Orientation Diagnostics and Align 3D Maps, all produce one or more volume outputs. Where multiple volumes are produced, each is output separately, e.g. Volume class 0, Volume class 1, etc.

In v4.5+, the above job types also produce a Volumes group output, denoted by the type volume_multi, which contains multiple volumes in a single output. Some jobs in v4.5+ also take volumes groups as input.

Unlike an individual volume output, a volumes group can contain an arbitrary number of volumes unknown at the job’s build time, can include multiple versions of each volume such as map and map_sharp, and can also contain metadata information about each of those volumes such as resolution info.

For jobs that produces many volumes in a volumes group, all the volumes can be connected to a downstream job with a single connection of the volumes group, rather than many individual drag-and-drop actions to connect each individual volume. Volumes group connections can also be used when setting up Workflows.

Note that a volumes group (volume_multi type) is not the same as an individual 3D volume output (volume type). These two types cannot be interchanged, and jobs requiring volume_multi as input can not take in volume inputs. Jobs run in CryoSPARC versions prior to v4.5 do not produce volumes group outputs and therefore cannot be connected to jobs that require volumes group inputs in v4.5+.

volume_multi outputs have a new output field, alignments3D_multi. We do not expect users will need to interact with this field in typical CryoSPARC usage, but some external software (such as pyem) may need to be updated to handle the new data format.

When to use Split Volumes Groups

Split Volumes Groups can be used with any job that produces a volumes group in order to separate the volumes from the group into individual volume outputs, as well as associated particle outputs if a particle stack is provided. For example:

• After Reference Based Auto Select 3D, use Split Volumes Groups to split apart the Volumes selected output into individual volumes, so that a particular volume can be used for refinement.

• After 3D Variability Display, use Split Volumes Groups to split apart one of the Volume series outputs in order to use a few volumes from different positions along the 3D variability components as input volumes for Heterogeneous Refinement or 3D Classification.

Inputs

All particles

This is an optional input. If provided, particles require 3D alignments corresponding to the volumes group to be split, and so should come from the same job that produced the volumes group connected to the All volumes input.

All volumes

The volumes group to be split. This group can contain an arbitrary number of volumes. If the group contains multiple versions of each volume (e.g., map , map_sharp, etc.), then all versions of each volume will be output in each of the individual volume outputs.

Commonly Adjusted Parameters

Static number of output volumes

This is an optional parameter. Fix the number of single volume outputs this job will produce, regardless of how many volumes are in the input group. When this parameter is set to N, the first N volumes from the input volumes group will be produced as individual output volumes.

This parameter is necessary for using the Split Volumes Group job in Workflows, so that volume outputs from this job are available for making connections downstream before this job is actually run. If there are more volumes present in the input group than this parameter, the extras will not be output; if there are fewer volumes present, the job will contain some unpopulated outputs. When not set, the job will dynamically produce volume outputs at run time.

Outputs

Particles class X

This output is only produced if particles were connected to the All particles input.

Subset of input particles that correspond to class X.

Volume class X

An individual volume output containing all versions of the volume for class X.

Downloading a volumes group: series

Note that some jobs that output volumes groups also provide a series result as part of the volumes group. The series (or series_sharp, etc.) results serve as a convenient way to download a zip file containing all of the volumes in the group, for visualization: