[ome-users] Problem importing multi-page tif

[Curtis Rueden]

Hi Hermann-Josef and Michael,

Michael wrote:
> Would you please tell me how to send you sample files

Files up to 2GB can be sent to the Bio-Formats team using the OME QA system:

http://qa.openmicroscopy.org.uk/qa/upload/

Please also follow up with a mail explaining what you uploaded and why.

Hermann-Josef wrote:
> Once it is fixed, will this automatically mean that the fix will be
> implemented into bio-formats?

Not automatically, although the SCIFIO developers will communicate details
of the fix to the Bio-Formats team, to facilitate a similar bug-fix on that
end.

That said, I doubt we will have time to pursue a fix for this issue within
the next six months, unfortunately. But in the meantime, a PR from a
motivated developer would be very welcome.

Regards,
Curtis

On Thu, Sep 24, 2015 at 12:41 PM, Cammer, Michael <
Michael.Cammer at med.nyu.edu> wrote:

> Would you please tell me how to send you sample files to check for:
>
> 1.  ND2 files not being opened completely.
>
> 2.  CZI files having various issues.
>
> 3.  TIFF files exported from Zeiss Blue opening in Photoshop but not with
> IJ.
>
>
>
> Thank you!
>
>
>
> =========================================================================
>
> Michael Cammer, Microscopy Core & Skirball Institute, NYU Langone Medical
> Center
>
>                       Cell:  914-309-3270     ** *MY OFFICE HAS MOVED TO
> SKIRBALL 2nd FLOOR, Back right ***
>
>           http://ocs.med.nyu.edu/microscopy & http://microscopynotes.com/
>
>
>
> *From:* ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] *On
> Behalf Of *Curtis Rueden
> *Sent:* Thursday, September 24, 2015 1:20 PM
> *To:* OME User Support List
> *Subject:* Re: [ome-users] Problem importing multi-page tif
>
>
>
> Hi Hermann-Josef,
>
>
>
> Thanks for the sample. I added it to our collection for SCIFIO, where we
> already have an issue filed for this problem:
>
>
>
>   https://github.com/scifio/scifio/issues/159
>
>
>
> In your case, it's a different bit depths rather than different
> dimensions, but the problem is the effectively the same.
>
>
>
> Sorry to say I don't have a timeline for fixing this, but it's on our
> radar.
>
>
>
> On the Bio-Formats side, I'm not sure whether there is an issue tracking
> this limitation yet.
>
>
>
> Regards,
>
> Curtis
>
>
>
> On Thu, Sep 24, 2015 at 10:08 AM, <posts at roeser-reichartshausen.de> wrote:
>
> Hi Curtis,
>
> a sample image is on my server:
> http://www.roeser-reichartshausen.de/Scans/Test.tif (250 MB)
>
> Thank you for looking into this.
>
> Hermann-Josef
>
>
> Zitat von Curtis Rueden <ctrueden at wisc.edu>:
>
>
>
> Hi Hermann-Josef,
>
> Can you share a sample image?
>
> Regards,
> Curtis
>
> On Thu, Sep 24, 2015 at 3:42 AM, <posts at roeser-reichartshausen.de> wrote:
>
>
> Hello,
>
> my multi-page tif image, created with imagemagick, contains a 3x16bit RGB
> image on page 1 and a 1x16bit B&W image on page 2. This image is not
> correctly imported with bio-formats 5.1.4 into imageJ. However, it is
> correctly opened in GIMP2 and IrfanView. So I suspect, there is a problem
> with bio-formats input. However, other images with the same structure but
> from a source different to imagemagick are imported correctly.
>
> Does anybody know this problem and a possible solution?
>
> Hermann-Josef
>
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