Posted by
Rasband, Wayne (NIH/NIMH) [E] on
Jun 08, 2015; 4:55pm
URL: http://imagej.273.s1.nabble.com/ImageJ-loading-of-BigTiff-files-VERY-slow-tp5013062p5013073.html
> On Jun 8, 2015, at 5:15 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.
This sounds like a Bio-Formats issue so downgrading to ImageJ 1.49s should not make a difference. What version of Bio-Formats are you using? The current version is 5.1.2. Use the Help>About Plugins>Bio-Formats Plugins command to get the version. Bio-Formats issues should be brought up on the ome-users mailing list at
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users/Have you tried the File>Import>Image Sequence command? It should be much faster. Make sure “Use SCIFIO when opening files” is disabled in Edit>Options>ImageJ2.
-wayne
>
> 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
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