Focal stacking of images in R/EBImage
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phil.chapman ▴ 150
@philchapman-8324
Last seen 4.8 years ago
United Kingdom

Has anyone got experience of carrying out a focal stacking operation on an image stack in R?  This is where one has a series of images with the same field of view but different focal planes, and these are combined into a single image where everything is magically in focus.

Thanks, Phil

ebimage • 1.1k views
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Bernd Fischer ▴ 540
@bernd-fischer-5348
Last seen 4.6 years ago
Germany / Heidelberg / DKFZ

The easiest way to combine images from a confocal microscope is a max-projection, which can be obtained by

Img = readImage(c("img1.tif","img2.tif","img3.tif","img4.tif"))

MaxProj = apply(Img, 1:2, max)

display(MaxProj)

In many cases this is sufficient. However, other algorithms are not available in R.

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Thanks Bernd!  So you're just taking the maximum intensity for each pixel?

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Hi Phil, this method is now provided by the new Bioconductor package MaxContrastProjection. The package also implements the novel maximum contrast projection algorithm which avoids some of the problems of the former method and yields cleaner results.

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Andrzej Oleś ▴ 750
@andrzej-oles-5540
Last seen 8 months ago
Heidelberg, Germany

Hi Phil,

focus stacking is now provided by the Bioconductor package MaxContrastProjection. It implements various projections methods of 3D image stack along the z-dimension into 2D, including the maximum intensity projection, and a novel maximum contrast projection algorithm.

An alternative would be to try some third-party tools, see e.g. this list.