Minor bug with Aperio Images with fractional objectives

Derek Magee D.R.Magee at leeds.ac.uk
Mon Mar 21 23:35:12 EDT 2016

-----Original Message-----
From: openslide-users [mailto:openslide-users-bounces+d.r.magee=leeds.ac.uk at lists.andrew.cmu.edu] On Behalf Of Benjamin Gilbert via openslide-users
Sent: 22 March 2016 16:26
To: openslide-users at lists.andrew.cmu.edu
Subject: Re: Minor bug with Aperio Images with fractional objectives

On Tue, Mar 22, 2016 at 02:57:30AM +0000, Derek Magee via openslide-users wrote:
> This is a minor bug as the only images with non-integer objectives 
> I've ever seen were generated by me, but with Aperio .svs if the 
> objective (i.e.  AppMag) is non-integer openslide.objective-power is 
> not output by openslide as part of the output of openslide_get_property_names().
> ImageScope simply rounds these to integer.  Happy to provide such a 
> file if people think it's worth fixing (I can probably work around it).

>Hi Derek,
>Yep, OpenSlide parses AppMag as integer, and doesn't add the generic property if parsing fails.  How did you produce the affected slides?  Were they actually scanned with non-integer objectives?

They are the result of image analysis where there is a downsample as the first step => 20X image becomes 2.5X if downsampled by a power of 2 factor 3 times. Power of 2 downsampling is a fairly sensible thing to do, but you quickly get to non-integer objective. I'd say even if you objected to non-integer objectives (I don't see why), the Aperio strategy of Rounding at least gives some clue. I personally use it to work out the ratio between original and downsampled versions (although I could just use mpp-x, or mpp-y equally as well). It's not a major problem for me now I know it happens, but it may trip up others.


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