my cancer chronicle: methodology

This page illustrates a bit how I gathered the data presented in the my cancer chronicle. As I mention in this other page, in Flanders, Belgium - where I live - patients can have access to their medical data through a digital collaboration platform called CoZo. Different types of data can be found there:

imaging data: from DICOM to open format

Now, I was particularly interested in the imaging data. If you are navigating CoZo, imaging datasets are displayed in a third-party platform called Sectra Uniview. The experience online is really smooth (though it’s always best to let a physician walk you through medical data), and from there you can even download a full set of images.

This is great, of course, even though the only way to download the images is in the DICOM format. DICOM is the standard format for Digital Imaging and Communications in Medicine that makes sure that different imaging machines and software from different manufacturers (like CT scanners, MRIs, X-ray machines, and computers) can easily read, store, and share the same images and patient data with each other. In one word: interoperability. I LOVE IT!

However, because the format contains image data along with patients metadata, you just can’t go ahead and open an image like you normally would. There are open source viewers available online, but I really wanted to have access to the pixels (you’ll see why later on), so I used the pydicom open source library.

It’s really easy to use, you can find a rather trivial script here.