Job: Blob Picker
Blob-based picking.
Description
Automatically picks particles by searching for Gaussian signals.
Input
Aligned/motion-corrected micrographs
Common Parameters
Use circular, elliptical, or ring blob
Blob picker can generate circular blobs (best for generally globular targets), elliptical blobs (best for rod or disk shaped targets), or ring blobs (best for hollow targets). Because of differental normalization between the blob types, we generally recommend only one mode is used in an individual Blob Picker job. Picks from different modes can be combined in subsequent steps.
Minimum / Maximum particle diameter (A)
Blobs are generated with sizes varying one dimension of the blob between these two sizes in Å. The exact behavior of the parameters differs in the three Blob Picker modes and between CryoSPARC versions before or after v5.
Circular blob
A number of circular Gaussian blobs between the minimum and maximum diameters are generated. In CryoSPARC versions before v5, Blob Picker always generated three blobs: one at the minimum, one at the maximum, and one halfway between the two.
Starting with CryoSPARC v5, between 2 and 10 circular blobs are generated as determined by the minimum and maximum diameter and Blob size spacing (A).
Elliptical blob
Elliptical blob(s) are generated. In versions of CryoSPARC before v5, only a single blob was generated with Minimum particle diameter controlling the minor axis and Maximum particle diameter controlling the major axis.
Starting with CryoSPARC v5, between 2 and 10 elliptical blobs are generated, controlled by Ellipse generation mode and Blob size spacing (A).
If Ellipse generation mode is set to "Stretch", ellipses start as a circle with radius Minimum particle diameter. The major axis then increases in steps of at least Blob size spacing until it is equal to the Maximum particle diameter. The generated templates are most useful for rod-shaped objects.
If Ellipse generation mode is set to "Squeeze", ellipses start as a circle with radius Maximum particle diameter. The minor axis is then reduced in steps of at least Blob size spacing (A) until it is equal to Minimum particle diameter. The generated templates are most useful for flat, disk-shaped objects.
Note that no ellipse generation mode varies both axes — one is always fixed.
Ring blob
A single ring blob is generated. From the center to a distance of Minimum particle diamater / 2, the template has a value of 0. From Minimum particle diameter / 2 to Maximum particle diameter / 2 the template has a value of 1.0. Further than Maximum particle diameter / 2 the template is 0 again. Put another way, the ring has density in the circles with a diameter between the minimum and maximum values.
Blob size spacing (A)
New in CryoSPARC v5
As described in Minimum / Maximum particle diameter (A), the number and shape of blobs is in part controlled by this parameter. If left blank (default), a value of 20 Å is used. If more than 10 blobs would be generated with the combination of Minimum and Maximum particle diameter and Blob size spacing, Blob size spacing is adjusted such that 10 blobs are generated.
Pick on denoised micrographs
By default, Blob Picker will pick particles on raw micrographs even if denoised micrographs are available. Turning this parameter on will pick particles using the denoised micrographs. In almost all cases, particles picked on denoised micrographs are higher quality than particles picked on raw micrographs.
Regardless of this setting, particles will ultimately be extracted from the raw micrographs.
Output
Particles
Notes and Limitations
Blob picking is a fast picking method but is generally the least accurate. This accuracy issue stems from being overambitious in micrographs featuring Gaussian shaped particles, and performing poorly on micrographs that lack Gaussian-like particles. The former is caused by the blob picker picking all Gaussians, regardless of whether they are particles or not. However, the incorrect particles can be filtered using a combination of the 2D Classification and Select 2D jobs.
Common Next Steps
2D Classification and Select 2D to generate templates for Template picking
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