What is Scalismo?

Welcome. Before we start on shape modelling code concepts, I would like to take a few minutes to introduce you to Scalismo. So, Scalismo is a software library that provides you with tools for medical image analysis and shape modelling. The fact that it’s a software library means that you can either build your own application on top of it. Or you can integrate it into bigger software projects. Scalismo is also open source. And it is distributed under the Apache 2 licence. The fact that it’s open source means that you’re free to use it and distribute it. And this including for commercial purposes. And it also means that you’re welcome to contribute and help make it better.

So, what are the functionalities of Scalismo? Well, the main functionality is, of course, shape modelling. Using Scalismo, you can build free-form deformation models where you can tune the properties of your model. Or you can also learn the deformations from data, as the case of this face model here. You can also fit the shape models to image data and surface data. And we will see how to perform all these tasks in the coming weeks. In addition to shape modelling, Scalismo also supports 2 and 3D medical image analysis and allows you to perform image-to-image registration. It also allows you to manipulate 3D surfaces that can come either in the form of triangle meshes or point clouds.

And it also provides you tools to perform mesh-to-mesh registration. In this course, you will be using a tool called Scalismo Lab. This is one executable that packages the entire functionality of Scalismo. And it is the best tool to start learning Scalismo. It is also thought as a tool to quickly try out small applications. All the scripts that you will write in Scalismo Lab can then be used into a larger Scalismo projects. This tool also ships with all the tutorial documents that we will use in this course. After watching the video tutorials, we strongly recommend that you go through these documents for yourself and give the tutorial a try. Scalismo is written in Scala.

Scala is a modern programming language that runs on the Java virtual machine. Scala is both object oriented and functional, which makes it close to mathematics. It is also a language that is both compiled and scriptable. And all these properties make it a scalable programming language that can be used to write programmes that are either small scripts or large, heavy duty applications. Now, you might ask yourself, do I have to learn new programming language in order to follow this course? Well, the answer is not really. First of all, we try to keep the Scala code simple. Also, all the example code that you will see in this tutorial can be executed directly without needing to know the details of Scala.

We also provide you with a small Scala cheat sheet as a quick reference guide to Scala. This said, if you would like to continue using Scalismo after this course, then we do recommend that learn Scala. From now on I will be seeing you in the tutorial mode, where we will be using Scalismo Lab together. I hope that you will enjoy the coming weeks coding together. And I hope to see you in the tutorial.