Reviewing the results of an image based experiment, across many images, can be annoying in matlab. Too much clicking!
I’ve recently started using PowerPoint to view many of my results. This blog posts discuss how using the free export to PowerPoint toolbox it is possible to create a slide desk with all relevant information for easier viewing. It looks like this:
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.
Continue reading Import Annotations from Matlab into BigTiff XML (Ventana)
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.
Continue reading Extract Annotations From ImageViewer Bigtiff xml into Matlab
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.
Continue reading Working with Aperio SVS files in Matlab – Converting Annotations to Binary Masks
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.
Continue reading Stain Normalization for Histology Images