OME-TIFF and ImageJ

I have created a OME tiff file (‘album’) that contains images of a sample taken at different magnifications and sample positions. If I open this file in uM, the correct pixel calibration is applied to each file and also the used LUT is reapplied on a per image basis. If I open this file in ImageJ, the calibration of the 1. image in the stack is applied to all images and an average LUT scaling is used resulting in over and underexposed images. Is there anything I can do so that the files open the same in ImageJ as in uM? Most users do not have the uM software on their pc.

HI @cparker,

I don’t know enough about ImageJ to be certain, but I don’t think that ImageJ has a mechanism to use per image (rather than per stack) pixel size data. It is actually already quite an impressive hack for these files to contain metadata for three different systems (Micro-Manager, ImageJ, and OME). If your users need this, I would advice them to install Micro-Manager (free download). I find its viewer also to be much nicer than the standard ImageJ viewer.

Good to know and no problem to recommend Micro-Manager for the users. I also verified that the scaling metadata is indeed in the tif file itself and not only in the sidecar metadata txt file. This is important since users might tend to get rid of the extra files. Btw, is there a way to store files without creating a folder for each tif or album?

Not that I am aware of.

I also dislike the fact that each image file is saved in its own folder. If you prefer to have all images from an experiment together in a single directory, you can use this simple bash script (on linux or Mac) to move them to the root folder after you’re done acquiring:

for folder in ; do
if [ -d “$folder” ] # Make sure this is a directory
for file in “$folder”/
; do
mv “$file” “.”;
rmdir “$folder”;

Make sure you navigate to the root image directory (i.e., the folder of image folders) before running this. I don’t know of an alternative that will work on Windows.

Dan Dickinson

Thank you Dan! Windows 10 has WSL, a linux shell inside windows, so this can also work on windows. Not sure yet how I deal with the folders. Moving all the files out of the folders seems like a good idea. During the work on the microscope it doesnt matter that the images are in seperate folders.