Problem opening a series of tiff stacks with very large files
Posted by Ryan Simmons on Mar 16, 2015; 4:09am
URL: http://imagej.273.s1.nabble.com/Problem-opening-a-series-of-tiff-stacks-with-very-large-files-tp5011978.html
Hello,
I have been having trouble opening a series of tiff stacks in FIJI. The data is comprised of high-resolution, 32-bit fluorescent images with the z-stacks in the area of 110 per movie. Each movie was acquired with two channels, but with the size of each tiff stack often being around 6 GB, making the two-channel tiff stack require up to 12 GB of our lab computer's 16 GB. I usually open smaller series of files (~1GB) as tiff hyperstacks with the Bioformats importer tool, but when trying to open the larger data sets this same way, FIJI often crashes. When it is able to open the entire hyperstack this way, the z-stack for the first time point is okay but the z-stack for all the following time points is just a replicate of the first. I have set FIJI to use as much ram as possible but it seems unable to open the data this way. The only way I have been able to open these movies in their entirety is to write a macro to open and convert each file to 16-bit and re-save them, then open just a few stacks (about 1/8 of the time points at a time), concatenate them, save that as a new tiff stack and repeat. That is followed by concatenating the concatenated smaller stacks, then converting to a hyperstack and saving as a tiff. FIJI has no problems opening these tiff hyperstacks, but this process is time-consuming and requires degrading the data from 32-bit to 16-bit. I would greatly appreciate any insight as to whether there is a better/faster way to open such large files in FIJI. Also I would like to know whether or not FIJI/ImageJ is capable of handling so much data or if other programs like Amira/Imaris can deal with such data more easily.
Thank you very much,
Ryan Simmons