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
>
>
>
> --
> View this message in context:
>
http://imagej.1557.x6.nabble.com/Problem-opening-a-series-of-tiff-stacks-with-very-large-files-tp5011978.html> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html
Locked
