Looking into brains – from numbers to images
by Cornelia Weigelt
Fourteen eager youngsters were taken on a trip into the world of programming at our Institute in early June. This was one of the Kids University workshops offered by Max Planck Institute for Neurological Research. In teams of two, overseen by qualified supervisors, they entered this new realm and learnt to navigate through it with the help of the programming language Python.
A bold plan - to interest children in just two hours in programming and selected aspects of imaging using real data from our routine scientific work. The plan, devised by the project initiator Stefan Vollmar, requires the help of several colleagues to supervise the course, enough computers for “trying yourself” and exercises and examples, assembled on a CD-ROM, for each child to take away for further study at home.
The most important tools for the course are seven well-equipped Apple iMac systems that are put straight to use with no hesitation. The warm-up task is: take a photo of yourself, store it and find it again. Got that - then you’re familiar with the keyboard and data storage. The Course Leader then asks, “What’s one and one?”. Naturally, all the kids know the right answer, only the computer gets it wrong: Syntax Error. Ah … so programming depends on correct formulation, otherwise the PC will not understand the question.
The next exercise is a playful demonstration of the idea behind “loops”: these constructions are used in programming languages to avoid having to go through repetitive steps again and again by hand. Understood? Then it goes ahead in leaps and bounds and within one and a half hours the kids are doing simple segmentation exercises: sorting colours according to their threshold values. The course materials come from specially prepared raw data from the logo of the Kids University event, the Kölner KinderUni “Owl”, whose individual parts (eyes, wings) can be coloured in using a few lines of programming. The “grey” owl introduces the kids to visualization with colour tables, before they move on to handling “real” data from human brains.
The course deals with data from two different imaging techniques (MRI and PET). Short sample programs transform the data from corresponding sections of the brain into images, first using a grey scale and then a red one. The data all come from the same human brain, acquired by two different scanners. A further short program allows the sections from the two scanners to be fused into a single image, thus combining the strengths of the two imaging techniques. Before images can be fused in this way, the data sets must be properly aligned in a pre-processing step.
Finally, all the participants are set a search task. “Find the Eyes!” is the order. This can be solved using a software package (VINCI; also on the CD-ROM) developed at the institute for visualization of sets of brain data. And away they go: Start the program, load in the 3-dimensional data record, move through the brain until you get to the right section. “Bingo!” On this successful note, the session ends. Just in time, as some kids are beginning to show signs of strain from the mental effort. Just one quick souvenir photo, signing in the Visitors Book, stamping of the course book and then it’s off home – CD-ROM in the hand to carry on. The ambitious plan has worked out – the Course Leader and his assistants look tired but well satisfied with the outcome.
