Assuming we have the necessary files on our Bisque server (perhaps uploaded with our script), and we have a set of bisque compliant XML annotations (perhaps generated with our script), we would like to upload them to the Bisque server so that they can be evaluated or modified. That is what this post is about  🙂
Uploading Files to Bisque via Python
In this blog post, we discuss how to quickly upload a dataset to Bisque using python. The next blog post will then talk about how to convert binary masks (made in matlab) to annotations usable by Bisque for validation or modification.
Import Annotations from Matlab into BigTiff XML (Ventana)
In the previous post  we discussed how to export annotations from a Ventana Image Viewer program and create binary masks. Now we explain how to do the opposite and import the mask back into Image Viewer.
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Extract Annotations From ImageViewer Bigtiff xml into Matlab
Previously we looked at extracting annotations from Aperio Svs files. There are other image formats and annotation tools. Another commonly used tool in digital histology is ImageViewer, which makes it possible to view multi-page BigTiff image files.
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Overlaying Binary Masks on Images in Matlab
There are often times when we want to see the boundaries of an annotation overlaid on an image for easier inspection. Using the ‘AlphaData’ layer in matlab this becomes extremely easy and efficient.
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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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Stain Normalization for Histology Images
I’m trying out the stain normalization toolbox provided by the Department of Computer Science over at Warwick . Be fair warned, it’s a windows only, matlab, toolbox.
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