Focal stacking of images in R/EBImage
2
0
Entering edit mode
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
ADD COMMENT
2
Entering edit mode
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.

 

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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 REPLY
1
Entering edit mode
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.

ADD COMMENT

Login before adding your answer.

Traffic: 557 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6