Failed to get correct layer count for Aperio images

[Ginger Han]

Thanks for your reply.

I was able to print out the actual error:

Cannot read this file because your OS vendor ships a modified version of OpenJPEG with broken support for chroma-subsampled images.  OpenJPEG error: Error decoding tile. Component 1 contains only 32768 blocks while component 0 has 65536 blocks

Then I searched for this error and found out it is due to OpenJPEG patch.

I have OpenJPEG 1.5.1-10.el7, OpenSlide 3.4.1-.el7 installed on my RedHat server.

Should I downgrade OpenJPEG to a version lower than 1.3.1 as suggested in the bug post: 

https://lists.andrew.cmu.edu/pipermail/openslide-users/2014-March/000751.html <https://lists.andrew.cmu.edu/pipermail/openslide-users/2014-March/000751.html>

OR…. should I upgrade OpenJPEG to 2.1.0????



> On Mar 22, 2016, at 3:34 PM, Rogers, David W <drogers at fredhutch.org> wrote:
> 
> Openslide documentation indicates that all levels other than level 0 are ignored for some formats, e.g., Hamamatsu. Perhaps it is the same for Aperio?
>  
> --
> David W. Rogers 
> Software Developer / Collaborative Data Services / 206.667.7089 / drogers@fredhutch.org <http://fredhutch.org/> / Fred Hutch / Cures Start Here
>  
> From: openslide-users [mailto:openslide-users-bounces+drogers=fredhutch.org at lists.andrew.cmu.edu] On Behalf Of Ginger Han via openslide-users
> Sent: Tuesday, March 22, 2016 11:54 AM
> To: openslide-users at lists.andrew.cmu.edu
> Subject: Failed to get correct layer count for Aperio images
>  
> Hello,
>  
> I have a collection of Aperio whole slide images of digital pathology. None of them was successfully read using OpenSlide C API functions. 
>  
> For example, with openslide_get_level_count()  I only get -1 for layer count indicating that the reading was not right.
>  
> However, ALL of them can be opened using Aperio ImageScope without any problem.
>  
> Please help!!!!

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