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Question: Focal stacking of images in R/EBImage
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gravatar for phil.chapman
18 months ago by
phil.chapman120
United Kingdom
phil.chapman120 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

ADD COMMENTlink modified 18 months ago by Bernd Fischer540 • written 18 months ago by phil.chapman120
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gravatar for Bernd Fischer
18 months 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.

 

ADD COMMENTlink written 18 months ago by Bernd Fischer540

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

ADD REPLYlink written 18 months ago by phil.chapman120

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.

ADD REPLYlink modified 11 months ago • written 11 months ago by Andrzej Oleś680
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gravatar for Andrzej Oleś
18 months ago by
Andrzej Oleś680
EMBL Heidelberg, Germany
Andrzej Oleś680 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.

ADD COMMENTlink modified 11 months ago • written 18 months ago by Andrzej Oleś680
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