ish_image_processing

Tools for formatting Marmoset in situ hybridization images

Requirement

Install Fiji
Add this line to your .bashrc (not necessary but used in the following description):

alias imagej='/Applications/Fiji.app/Contents/MacOS/ImageJ-macosx'

Converting .scn files to .tif files
This macro makes filename.scn_rough.tiff from filename.scn.

$ imagej -macro ish_image_processing/ConvertSCNtoTIFF.txt [target_directory]

Trimming three images for each slide

This macro makes filename.scn_rough-[i].tif� from filename.scn_rough.tif where [i] = 1,2,3.

$ imagej -macro ish_image_processing/Trimming.txt [target_directory]

Rotating each images accuratery

This script updates filename.scn_rough-[i].tif� , and ignores the slide file filename.scn.

$ imagej -macro ish_image_processing/Rotate.txt [target_directory]