[ome-users] Slow reading of ome.tiff files

[Roger Leigh]

On 15/06/2015 11:50, Jan Eglinger wrote:
> since the 5.1.2 release of Bio-Formats, I experience a very slow reading
> of certain OME-TIFF files with the Bio-Formats importer in Fiji. A 400MB
> 2-channel 11000x9000 pixel 16-bit image (that was exported as ome.tiff
> from Zeiss ZEN software) takes more than 10 minutes to load, regardless
> of whether it is being read from local disk or network.
>
> The same file opens within seconds when using the Fiji Life-Line version
> from 2014 November 25 that ships with Bio-Formats plugins version 5.0.6.
>
> I'll upload one of the files to http://qa.openmicroscopy.org.uk/qa/upload/
>
> Did anyone else experience this behaviour?

I hadn't.  But it may be the image size/strip size of this TIFF trigger
pathological behaviour.  I can certainly reproduce this with the file
you uploaded, but only on Windows--the image takes just 5s on MacOS X
but ~30 mins on Windows 8.1!

I have opened a ticket for this here:
https://trac.openmicroscopy.org/ome/ticket/12930 with the current
details.  We'll need to pin down exactly when the regression happened
and what exactly the cause is.


Kind regards,
Roger

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096