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📝 Workshop on medical image segmentation

teaching university students about medical image segmentation in Python

Me and Alexandre Calado had the opportunity to teach a small course on medical image segmentation at a small student conference organised by the Núcleo de Estudantes do Departamento de Física at Universidade de Coimbra.

It was a great opportunity to brush up on what we know and how we can best communicate it. Given that it was supposed to be a hands-on workshop, I thought that a small Kaggle notebook could be a great opportunity of getting everyone’s hands dirty with a club classic - the Medical Segmentation Decathlon. So I coded a small tutorial on medical image segmentation. It’s free to use with an Apache License 2.0, so feel free to use it with the appropriate attribution 🤗

📝 How to develop a radiomics signature

Presentation and workshop on applying machine-learning to radiology data to medical doctors + biomedical researchers

In 2024, I participated as faculty in the “How to develop a radiomics signature” course organised for the European Society of Gastrointestinal and Abdominal Radiology. Here, I gave a short presentation on machine-learning model development and tuning, as well as two practical programming sessions: one on radiomic feature extraction and the other on model development and (fine-)tuning. Both are freely available.

📝 EMBL Summer School

presentation and workshop on machine-learning applied to computer vision to young students

In the 2019 EMBL Lautenschlager Summer School, I talked about how to use random forests in an image segmentation context, covering at an introductory levels some aspects of image preprocessing, feature extraction (with some focus on gradient calculation) and the internal mechanics of random forests. During this time, I also aided in practical classes which focused on implementing a pipeline to analyse the growth of Nematostella.

📝 Basic Teaching Module at EMBL predoc course

workshop on computer vision feature extraction theory + applying machine-learning to simple biological problems

In the 2018 EMBL Predoc Course and with Julian Hennies, I talked about feature extraction in images and how this can be applied to segmentation problems. We also discussed, more generically, how machine-learning can be applied to some other biology problems.

📝 Workshops on introductory programming

teaching university students about programming and data-viz in python and R

In JEST, a junior enterprise providing pedagogical services in data-science, I had the opportunity to teach programming at a beginner level, with particular focus on R and Python. Within Python, apart from focusing on the basic aspect of it, I also had the opportunity to speak about more modern packages for interactive data visualization, such as plotly.