[ome-users] [bioformats] Incorrect data loading from TIF file.

[Roger Leigh]

On 16/11/2015 16:16, Stephane Dallongeville wrote:
> I attached a TIF file which does not open correctly using the latest
> version of Bio-Format. Note that older versions of Bio-Format loaded the
> file differently (data were different) but weren't correct either. Here
> is the original message from the user who generated the image :
>
> <<
> I use ndpisplit
> <http://www.imnc.in2p3.fr/pagesperso/deroulers/software/ndpitools/> under Linux
> to split an NDPI file. However, Icy (latest version) doesn't read these
> files correctly and shows weird colors. My first guess is that the files
> were not RGB, but the tool "identify" by ImageMagic says indeed
> "Colorspace: sRGB".
> I converted the image to YCrCb in MATLAB and I think it looks like the
> one showed by Icy.
> Icy shows it correctly when I open the ndpi file directly (if the image
> is not huge), but sometimes I'll prefer to open the split image.
> I attach an image that Icy can't read correctly.
>  >>
>
> Note that you can replace Icy by Fiji/ImageJ, i tested on both (using
> Bio-Formats importer) and the problem is the same.

Do you have a screenshot of how this file displays in

- the original NDPI file viewer
- in Icy

Would it be possible to upload a copy of the original NDPI file using
e.g. http://qa.openmicroscopy.org.uk/qa/upload/ so that we can take a
look?  While I can see from the TIFF you attached that it does indeed
use YCbCr, without having some basis for comparison with what it's
supposed to look like in its original form, it's difficult to know what
it should look like.  Screenshots of exactly what you see would be very
helpful.

I opened it in Fiji and it certainly looks wrong.  I've attached a
screenshot of how it appears viewed with "tiffgt", the libTIFF OpenGL
image viewer.  Is that how it should appear?


Thanks,
Roger Leigh

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
School 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
-------------- next part --------------
A non-text attachment was scrubbed...
Name: ndpi-ycbcr-tiffgt.png
Type: image/png
Size: 2012990 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20151117/d4aa24ff/attachment.png>