Openslide Usage

[John Stevenson-Hoare]

Unfortunately the XML that describes this information is excluded from the slide properties so this makes your job a lot harder. If you know that the image is a Leica SCN file then maybe you could open the file (as a BigTIFF) yourself and read out the ImageDescription tag from the zeroth IFD. This is XML and the <view> element in an <image> defines where the ROI is relative to the origin of the slide overview. This origin is at the top-left of the slide and the offsets and sizes are in nanometres.

Good luck,
John

From: openslide-users-bounces+john.stevenson-hoare=ffei.co.uk at lists.andrew.cmu.edu [mailto:openslide-users-bounces+john.stevenson-hoare=ffei.co.uk at lists.andrew.cmu.edu] On Behalf Of Nikolay Kladt
Sent: 07 November 2014 13:55
To: openslide-users at lists.andrew.cmu.edu
Subject: Openslide Usage

Hi everybody,

I have just started to use OpenSlide Python to look at Leica Slidescanner images. While the basic usage is very simple, there is one question for which I cannot seem to find the answer:

The scn file has multiple associated images (scanned ROIs) that have been scanned with identical resolution. How do I access individual images or get their bounds? It seems that the properties do not show the required information but the file format description includes multiple images.

I think I can work-around easily by a first-pass, detecting background pixels to obtain the ROIs on level zero using tiled reading, before actually doing anything else but it seems that this information is somewhere already... I am pretty sure I got confused somewhere..


If this is a problem of having test data, we can easily generate data sets that can be shared.

Best (and thanks for writing a very promising tool),

Niko

--
Dr. Nikolay Kladt
Image and Data Analyst, CECAD Imaging Facility
kladtn at uni-koeln.de<mailto:kladtn at uni-koeln.de>
++49 221 478 84028
https://www.linkedin.com/in/kladtn

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