http://imagej.273.s1.nabble.com/ImageJ-loading-of-BigTiff-files-VERY-slow-tp5013062p5013070.html
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.
> 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