[ome-users] Saving large files in ome.tif or ids/ics

[Roger Leigh]

On 30/04/2015 21:40, Jason Miller wrote:

Dear Jason,

> Similar to recent past posts on this list, I'm having trouble saving
> files that are > 4GB into ome.tif or IDS/ICS formats. I have a 5GB file,
> open as a virtual file, and when I go to export via Bioformats Exporter
> to IDS/ICS format, I get the following error:
[stacktrace]

For IDS/ICS, this was fixed in this PR last week:
   https://github.com/openmicroscopy/bioformats/pull/1738
I have tested this with >5GB images and it works correctly.

> When I go to export to ome.tif format, I get the same error previously
> reported on this list:
> loci.formats.FormatException: File is too large; call setBigTiff(true)
>
> Is it possible to retain the ome.tif format for >4GB? In my case, this
> is for importing into Huygens for deconvolution.

For plain (not OME) TIFF:
   https://github.com/openmicroscopy/bioformats/pull/1744

Both of the above fixes are in the newly-released Bio-Formats 5.1.1
release.  If using Fiji, you should automatically get this update; for
ImageJ you can download the updated plugin from
   http://downloads.openmicroscopy.org/bio-formats/5.1.1/

For OME-TIFF, it's not currently possible to enable BigTIFF when
exporting from ImageJ using the exporter dialogue.  For the plain TIFF
case, rather than relying on an API call to enable BigTIFF, we now
enable it if the image data is >4GiB or a "big" TIFF file extension such
as .btf, .tf8 or .tf2 is used.  We would like to do the same for
OME-TIFF, but this first requires updating the OME-TIFF specification
which currently only allows a .ome.tiff or .ome.tif file extension.
Once that's done, you would be able to use e.g. ".ome.btf" and get a
"big" OME-TIFF file.  However, this does require some consideration
since (for example) these files would not be readable with older
versions of Bio-Formats unless you renamed them to ".ome.tiff" after export.

To summarise, it isn't currently possible to export >4GB ome.tiff files
using the Bio-Formats Exporter.  It is possible via the Java API by
calling writer.setBigTiff(true) if this is an option for you.  This is a
known limitation which we are working on; see the discussion in the PR
#1744 above.

There is a ticket open here for this:
   https://trac.openmicroscopy.org/ome/ticket/12858
I can add you as a CC on it if you like, so you'll be kept up to date
with its progress?


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