Can anybody explain the algorithm behind the Extended Focal Imaging option available in Olympus CellSens? I understand that it is some form of z-stack projection that is performed before the image is saved, but I was wondering whether it works as a maximum intensity projection or something else.
This is the explanation in the CellSens manual, but it does not explain the exact mechanism: The EFI projection uses a series of
differently focused separate images (Focus series) to calculate a resulting image (EFI
image), that is focused in all of its parts.
The system we have is Olympus SpinSR10 with CellSens, but I assume this option exists also on other microscopes.
This sounds like a focus stacking option. Basically an algorithm determines the best focus plane from a Z stack and projects this as a combined best focus projection.
I recall this function on Nikon systems as Extended Depth Focus (EDF).
Hi Teo,
Thank you for the explanation. So if I understand it correctly, for each z-stack in the tile-scan, a whole single plane is selected, right? Do you know what exactly determines which plane is ‘the best’? Is it based on sharpness/intensity?
I am not sure this is relevant, but it reminds me of this (disclaimer I did a student project in this lab a long time ago):
In summary, take a Z stack, and then at each slice, keep only the pixels that are in focus. You can then compose a single slice with only the in focus information.
This is an excerpt of their webpage:
Due to the limited depth of field of brightfield microscopes, it is usually impossible to image large 3-D organisms and objects entirely in focus. By optically sectioning the specimen, however, the in-focus information at the specimen’s surface can be acquired over a range of images, which can then be processed to generate a single in-focus image.
And they have a paper that describes the algorithm in details.
