Handling stacks with ImageJ

The output file you got from the camera if a (very heavy) .tif file, which you cannot visualize using your typical photos app. This is because it is saved as a stack. A few steps are required to transform them into a format suitable for ncorr, which will be described below:

1. Download ImageJ from here (it is free and extremely useful)

2. Open your .tif file in ImageJ by dragging it on the interface. You can now see all the pictures of your stack by using the slider under the picture!

3. Convert your stack to 8-bit for easier handling with NCORR (Image -> Type -> 8-bit)

4. Open all the images in your stack in individual windows (Image -> Stacks -> Stack to images)

5. Save all the images in individual .tif files. Go to Plugins -> Macros -> Record and paste the following code:


    for (i=0; i<#NUMBER OF PICTURES IN STACK#; i++)

Please make sure to copy the entire destination folder adress in the code above, as well as the number of images in the stack.

6. Then, click Create and Run the script. You now have all your individual .tif files ready to be used in NCORR! If the 'saveAs' part results in a bug (which somehow sometimes happens), go to Plugins -> Macros -> Record, then save the picture manually and copy the command that should have appeard in the Record window (adapt it to the form presented above).

If needed, you can also crop your pictures (Image -> Crop), play with contrast, levels, etc. (all in the Image -> Adjust section).