Photoshop - combine red and green channel images into a merged image?

[JohnnyR]

I am a developmental biologist carrying out experiments on a type of microscope known as a Confocal Laser Scanning Microscope (CSLM). Basically, this is a microscope coupled to some lasers which allow fluorescently-labelled parts of a biological sample to be imaged in high detail.

 

For each sample there will be a set of two images produced, named and numbered as follows:

 

sample01_g.tif

sample01_r.tif

 

Each image represents one fluorescent wavelength and correspond to green ( g ) and red ( r ). These images are in rgb colour.

 

I want to produce a merge of these two channels to generate a new TIFF file such that:

 

Green channel is taken from sample01_g.tif

Red channel is taken from sample01_r.tif

 

Which would show me how the different channels co-localise, or not.

 

This is fine to do by hand in Photoshop, but takes a long time when you have a couple of hundred images to process. So, what I would like to do is write a script that batch automates the process, like a droplet. I have the process outlined below:

 

1. Create a new RGB TIFF called sample01_merge.tif

2. Take the green channel from sample01_g.tif and copy it to the green channel of sample01_merge.tif

3. Take the red channel from sample01_r.tif and copy it to the red channel of sample01_merge.tif

4. Save sample01_merge.tif into a folder named "Merged Images" on the desktop

5. Close the opened images

6. Go to next set of images –> sample02_g.tif and sample02_r.tif

7. Create a new RGB TIFF called sample02_merge.tif....and go through step 2-6, untill the last set of images has been processed.

 

I have never used Applescript before and would love to learn, but I am making slow progress and would like to have this problem solved sooner than I will be able to do so by myself. So... I was wondering if anyone could give me some advice on how to go about doing this?

 

Any help will be greatly appreciated!

 

Best regards,

John

[k3nny]

Hi, it sounds interesting. Which kinds of samples are you analyzing?

 

I'm not really familiar with AppleScript and I would recommend you to consider creating a shell script utilizing the freeware tool Imagemagick (section "Combining RGB Channel Images").

 

This shell script should do the conversion:

#!/bin/sh

dirMerged="Merged Images"
suffixMerged="_merge"

mkdir "$dirMerged"
# Separate red channel for images with suffix _r. Output in folder $dirMerged.
for img in *_r.tif; do
 convert "$img" -channel R -separate "$dirMerged"/"$img"
done
# Separate green channel for images with suffix _g. Output in folder $dirMerged.
for img in *_g.tif; do
 convert "$img" -channel G -separate "$dirMerged"/"$img"
done
# Combine red and green channels. Output in $dirMerged.
# Remove single channel images from $dirMerged.
cd "$dirMerged"
for img in *_r.tif; do
 img=${img%_r.*}
 convert "$img"_r.tif "$img"_g.tif -channel red,green -combine "${img}${suffixMerged}".tif
 rm "$img"_r.tif "$img"_g.tif
done

[JohnnyR]

It is cell samples from the retina of rats.

 

Thanks for your suggestion. I'm not familiar with imagemagick but I'll sure have a look at it now.

[k3nny]

I forgot to mention a thing. Imagemagick requires an additional installation argument for TIFF support.

 

I would recommend you to use homebrew to manage the installation.

After you set it up, enter "brew install imagemagick --with-libtiff" to set up imagemagick.

That should be all.