Focus stacks are useful for a variety of purposes in imaging. Recently, we have demonstrated that fluid flow can transport a sample through focus with nanometer accuracy. Using fluid flow, focus stacks of individual cells can be produced in a single millisecond at throughputs of 100's of focus stacks per second.
One application of focus stacks is to produce phase images (using the Transport of Intensity Equation) that quantify optical path differences across the cell. Phase images can be used to resolve cellular features that are not visible in bright-field images or to quantify cell morphology in depth.
Using the fluidics-based focus stack collecting microscope, we have a built a phase imaging flow cytometer that captures quantitative phase images of cells in flow.
S. S. Gorthi and E. Schonbrun, "Phase imaging flow cytometry using a focus-stack collecting microscope," Opt. Lett, 37, 707-709 (2012).