Issue with some Aperio SVS files

[Derek Magee]

On 05/06/2014 04:23, Benjamin Gilbert wrote:
> On 06/04/2014 10:28 AM, Derek Magee wrote:
>> 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).
> Right, those are the missing tiles.  It seems they are always on the
> right or bottom edge, and only in levels other than 0.  ImageScope is
> probably working around them by downsampling tiles from level 0.
>
> In general, OpenSlide tries to return slide data with a minimum of
> processing.  For example, we don't usually synthesize pyramid levels,
> even when the levels in the slide file are far apart.  That's why we're
> returning transparent here.  But in this case, it's clear what the slide
> file *meant* to say, and it's easier for us to fix the inconsistency
> than the application.  So perhaps we should revisit this.
>
> Derek, could you give a rough idea of how many slides you have with this
> problem?  Do you have slides where the transparent areas impinge on
> meaningful content, as opposed to the background color?  Can you send me
> a couple samples for testing?
>
i) No. Slides: I only spotted it when I visualised a gallery of 
thumbnails of about 1000 slides, so it's rare. I think about 6 in that 
set had issues like this (so <1%).
ii) All missing data was nearish the bottom - but not necessarily the 
last row (and appears to be non-tissue areas as far as I can tell), 
although sometimes it was fully transparent (displayed in red in my 
app), other times just black (indicating non-zero transparency).
iii) I've not seen the problem on level 0, just lower resolutions. 
Taking missing data from level 0 seems a sensible approach to me (and I 
guess that's what ImageScope is doing).
iv) I'll hightail you some representative examples.

Thanks

Derek