Question: Focal stacking of images in R/EBImage
0
2.5 years ago by
phil.chapman140
United Kingdom
phil.chapman140 wrote:

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

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modified 2.5 years ago by Bernd Fischer540 • written 2.5 years ago by phil.chapman140
Answer: Focal stacking of images in R/EBImage
2
2.5 years ago by
Bernd Fischer540
Germany / Heidelberg / DKFZ
Bernd Fischer540 wrote:

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.

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

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.

Answer: Focal stacking of images in R/EBImage
1
2.5 years ago by
Andrzej Oleś720
Heidelberg, Germany
Andrzej Oleś720 wrote:

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.