Skip to content

Focus stacking

This image above is a composite image derived from 12 images put through a focus stacking algorithm in Photoshop CS4 and I have to say I am impressed with the results. Using a Canon MP-E 65mm 1-5X macro lens wide open at f/2.8 to ensure the focal plane was as thin as possible, I captured 12 images in a row, altering only the plane of focus a few hundred micrometers at a time using a focusing rail. Then all images were imported and aligned using Photoshop’s align stack script, then focus stacked using the focus stacking feature in Photoshop CS4.


The animated gif above shows each frame that went into the focus stack so that you can appreciate how narrow the plane of focus was and how successful the overall result in the introductory image is. Needless to say, I’ll be playing with this feature more and more to increase my depth of field for insects and all other potential candidates for the Small Life category.

Focus stacking as a concept has actually been around for quite a while and I have experimented with a couple of different options to derive the desired images. Some options are quite good, like Helicon’s Focus, and others provide acceptable results, but are free like the Extended Depth of Field plugin for the wonderful image processing application ImageJ developed by the NIH‘s Wayne Rasband. Big shout out to Wayne who has helped so many bioscientists explore and communicate their data.

However, having focus stacking in as part of Adobe Photoshop is a big deal, especially given the scripts for image alignment. I’ve been talking on and off for a while now with some of the project managers and engineers at Adobe, including John Nack regarding them stepping into the scientific and forensic imaging markets and I hope this happens sooner rather than later. Scientists and engineers have been using Photoshop for their purposes for years now and it would be nice to have more tools built into the system to access the details behind many of the filters and image transformations. Adobe at least sees this market and since many of the tools are already built in, what is missing is a better interface to allow access to more image math, filter definitions and such. FFTs would also be a lovely improvement to other quantitative improvements for image operations.


Categories: Small Life.

Tags: , , , , ,

Comment Feed

11 Responses



Some HTML is OK

or, reply to this post via trackback.

Continuing the Discussion

  1. […] is a focus stacked image with three separate exposures in separate focal planes combined to make for a more extended depth […]

  2. […] focus stacked image of a hobo spider (Tegenaria agrestis) found in the casa Jones.  Below is a different […]

  3. […] as I bundled him into a sample jar and took him on a Saturday to the lab for photography and to focus stack with a Canon 1D Mk III and an Olympus […]

  4. […] similar to a common technique in confocal microscopy, maximal projection, but in reality is simple focus stacking.  The five images that made up the pentaptych above can be found […]

  5. […] some circles is focus stacking.  I’ve written about it before with for both histologic and non-histologic applications.  The results can be remarkably compelling, making optical images appear like […]

  6. […] Más información:  Jonesblog […]

  7. […] and we had some ideas on how to help them visualize and render these neurons.  It turns out that focus stacking is a rather effective way of rendering 3D problems in 2.5D that preserves far more detail than […]

  8. […] was scanned in with a scanning stage microscope at multiple planes throughout the tissue, then focus stacked to get as much of the image in focus as possible.  If this sort of thing really turns your crank, […]

  9. […] This is a fluorescently tagged primary visual cortex neuron from a light microscope capture of a brain slice preparation.  These data were focus stacked revealing a tremendous amount of detail including the spines.  Focus stacking is common method in confocal microscopy, but many folks do not realize that you can also do it with traditional light microscopy of just about anything using ImageJ or Adobe Photoshop.  See here for an example and discussion of focus stacking. […]

  10. […] this image was technically a little difficult as it is actually 3 separate images that have been focus stacked to get more of the animal in focus.  This means I pushed the shutter button 3 times while moving […]