Particle stacks vs. single images - cianfrocco-lab/Old-school-processing GitHub Wiki

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Within data processing, you will be interacting with single 2D images, stacks of 2D images, and 3D volumes.

###Single 2D images

Individual 2D images are files that have a single image with X & Y dimensions.

You will encounter this file type in the following ways:

• Micrographs collected from the electron microscope.
• Class averages or single particles copied out of a stack.

###Particle stacks

Stacks of particles are a single file that contains a series of individual 2D images housed within a single filename. This means that each individual 2D image has only X & Y dimensions, BUT, the stack is comprised of more than one (and possible thousands) of individual 2D images 'stack' up.

You will encounter this file type in the following ways:

• Particle stacks used for analysis/processing
• Projections or slices through a 3D model displayed in 2D
• Stacks of class averages from 2D classification analysis

###3D volumes

3D volumes are files that have X, Y, Z dimensions, and require 3D visualization software (e.g. UCSF Chimera).

You will encounter this mainly from 3D reconstructions from averaging over 2D particle images during 3D classification and refinement.