Posted by
ctrueden on
Jun 08, 2015; 4:58pm
URL: http://imagej.273.s1.nabble.com/ImageJ-loading-of-BigTiff-files-VERY-slow-tp5013062p5013075.html
Hi Laurent,
> When I use ‘Group files with similar names’ to open all files at once,
> this is very slow if the total size is more than a few GB.
You can troubleshoot why things are so slow using the instructions here:
http://imagej.net/Debugging#Debugging_JVM_hangs> The only solution I found is to downgrade to version 1.49s.
If you see an I/O performance difference between 1.49s and 1.49t, that is
vital (and rather surprising) information. Are you using the "Help > Update
ImageJ..." command to switch between them when testing?
Regards,
Curtis
On Mon, Jun 8, 2015 at 11:15 AM, Laurentius Henricus Holtzer <
[hidden email]> wrote:
> Hi,
>
> I have a similar problem, which might be related. I am using the
> BioFormats plugin to open large data sets. Those data sets consist of
> multiple regular tiff-files in which each tiff file contains an image stack
> for one time point. Each individual file has a size in the range of 50-300
> MB.
>
> When I use ‘Group files with similar names’ to open all files at once,
> this is very slow if the total size is more than a few GB. Like Bill I had
> to kill FIJI since the process was running for hours and FIJI was not
> responsive anymore. The thread killer didn’t work either.
>
> The only solution I found is to downgrade to version 1.49s.
>
> Cheers,
> Laurent
> > On Jun 5, 2015, at 11:37 PM, Bill N. Whitney - whitnewn <
>
[hidden email]> wrote:
> >
> > I am running ImageJ version 1.49t (from Fiji) on Windows 7.
> >
> > I am working with a microscope that creates image stacks and stores them
> as TIFF files.
> > Sometimes, the image stack files can get bigger than 4GB, so we can also
> create BigTiff files.
> >
> > I can load a REGULAR Tiff file into ImageJ in at most 30 seconds. A file
> right at the 4GB limit takes 20-30 seconds to load. Smaller files are
> faster.
> >
> > Even a small BigTiff format file ( 64 MB) takes much longer than this,
> roughly 120 - 180 seconds.
> >
> > It takes a long time for ImageJ to START processing the individual
> images (2-3 minutes), AND it takes a long time for ImageJ to process each
> individual image (~30 sec).
> >
> > For example, loading a 1.8GB BigTiff file takes about 4-5 hours to load.
> The same file, stored as regular Tiff, takes about 12 seconds.
> > I have a 5GB BigTiff file, and after letting it run for 3 hours, it had
> only processed 85 of 500 images, so I killed the process.
> >
> > Any insights into what is going on here? I can provide sample files if
> that would be helpful .....
> >
> > Thanks,
> > Bill
> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
>
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html