Re: ImageJ loading of BigTiff files VERY slow

Posted by ctrueden on Jun 08, 2015; 4:54pm
URL: http://imagej.273.s1.nabble.com/ImageJ-loading-of-BigTiff-files-VERY-slow-tp5013062p5013074.html

Hi Bill,

Using File > Open will use ImageJ 1.x's built-in TIFF reader when possible,
and fall back to other TIFF readers including the Bio-Formats plugins in
some cases.

Are you testing with File > Import > Bio-Formats in all scenarios? That
will compare apples to apples.

Are your files on a network drive? Or local storage? Currently, performance
can be much worse on a remote mounted file system.

You can also try opening with SCIFIO, using the File > Import > Image...
command, although that code may suffer from performance problems similar to
Bio-Formats at the moment. We have plans to make it much faster [1].

Lastly, see this page for ideas on how to debug why things are taking so
long:
   http://imagej.net/Debugging#Debugging_JVM_hangs

Regards,
Curtis

[1] https://github.com/scifio/scifio/issues/7

On Fri, 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
>
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