Using SCIFIO for reading Whole Slide Images at different resolutions.

Beginner Questions
1

Hi Everyone, I’m new to ITK and I am using SCIFIO to read in whole slide images from proprietary image formats: “.svs .vms .bif” etc. I want to know if it is possible to read the image in at a different resolution directly from the image file. For example, I know the image file stores the image pyramid so is it possible to set the itkImageFileReader to read one of the lower resolution layers rather the high resolution image? I can read in the full resolution image myself and then down-sample the image from that, but this seems redundant if a lower resolution image is already available.

Thanks.

2

@ctrueden might be able to answer that.

3

Okay so I’ve managed to read in the file at a lower resolution using itkOpenSlideImageIO directly and setting the imageFileReader imageIO manually. The structure looked like this:

#include "itkOpenSlideImageIO.h" 

ReaderType::Pointer reader = ReaderType::New();
using OpenSlideIO = itk::OpenSlideImageIO;
OpenSlideIO::Pointer OS = OpenSlideIO::New();
OS->SetFileName(fileName);
OS->SetLevel(1);

reader->SetImageIO(OS);
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