Tools for formatting Marmoset in situ hybridization images
- 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]