Category Archives: Digital Histology

Working with Aperio SVS files in Matlab – Converting Annotations to Binary Masks

One of the main purposes of having a digital format is to allow experts (e.g., pathologists) to annotate certain structures in the images. Be it nuclei, epithelium/stroma regions, tumor/non-tumor tissue etc. This is easily done with ImageScope and SVS files, but the trick is importing them into Matlab.
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Working with Aperio SVS files in Matlab – Loading Sub-Sections

In the previous tutorial we discussed how to load different levels of the image pyramid for Aperio SVS images in Matlab and how they corresponded.

In this tutorial we will extend upon that in 2 critical ways. First, we’d like to be able to load only small sub-sections from images (easy) and then extend upon that so we can identify regions at a low-magnification that we’d like to load the corresponding high-magnification version (harder).
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Working with Aperio SVS files in Matlab – Introduction

Aperio scanners generate a semi-proprietary file format called SVS. At its heart, SVS files are really a multi-page tiff file storing a pyramid of smaller tiff files of the original image. We’ll look at those here using a SVS file provided by the TCGA (http://cancergenome.nih.gov/) breast cancer cohort:

TCGA-A1-A0SD-01Z-00-DX1.DB17BFA9-D951-42A8-91D2-F4C2EBC6EB9F.svs

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