Re: Problem opening a series of tiff stacks with very large files

Posted by ctrueden on Mar 16, 2015; 2:48pm
URL: http://imagej.273.s1.nabble.com/Problem-opening-a-series-of-tiff-stacks-with-very-large-files-tp5011978p5011987.html

Hi Ryan,

> I would greatly appreciate any insight as to whether there is a
> better/faster way to open such large files in FIJI.

Why not use the "Use virtual stack" option which opens image planes on
demand as you browse/need them?

Regards,
Curtis

On Sun, Mar 15, 2015 at 11:09 PM, Ryan Simmons <[hidden email]>
wrote:

> 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
>
>
>
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