Issue with some Aperio SVS files

[Derek Magee]

Benjamin,



A lot better thanks, however one remaining issue is that the bottom of the image appears to have missing tiles at low zoom which are output as transparent (see below - I made transparent pixels red to check it wasn't just outputting black).There is also a dark line at the border of these tiles it seems.

[cid:image001.png at 01CF7E9F.0EE3E570]



Whereas in ImageScope you don't get this and there appears to be data (or at least if it is filling missing data it is doing it in a very clever way as the background is far from 255,255,255):

[cid:image002.png at 01CF7E9F.0EE3E570]

Thanks



Derek



-----Original Message-----
From: openslide-users-bounces+d.r.magee=leeds.ac.uk at lists.andrew.cmu.edu [mailto:openslide-users-bounces+d.r.magee=leeds.ac.uk at lists.andrew.cmu.edu] On Behalf Of Benjamin Gilbert
Sent: 02 June 2014 00:19
To: openslide-users at lists.andrew.cmu.edu
Subject: Re: Issue with some Aperio SVS files



On 06/01/2014 07:02 PM, Derek Magee wrote:

> For some (say 1-2% of the ones I've tried) Aperio svs files, Openslide

> throws and error on openslide_read_region(). Metadata can be read ok,

> as can label images. Error printed out:

>

> TIFFFillTile: 0: Invalid tile byte count, tile 75



Some Aperio slides contain zero-length tiles; it seems to be a bug in some versions of the scanner software.  Fixed in this commit:



https://github.com/openslide/openslide/commit/7e033bbb



> I'm using openslide under windows (pre-built from a couple of months

> back).



Try a nightly build:



http://openslide.cs.cmu.edu/download/snapshots/windows/



--Benjamin Gilbert



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