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

Stephane Dallongeville stephane.dallongeville at pasteur.fr
Mon Nov 16 16:16:54 GMT 2015

Dear Bio-Formats experts,

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.


Stephane Dallongeville
Unité d'Analyse d'Images Biologiques
Institut Pasteur
25 rue du Dr. Roux
75724 Paris cedex 15 (FRANCE)

Tel: +33 (0)1 45 68 87 01
Fax: +33 (0)1 40 61 33 30


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