Note (2024-08-31): This post was written in February 2020. Support for building and deploying Jekyll sites on GitHub pages has been streamlined in the meantime and can now be performed with stock actions. See jekyll-build-pages and deploy-pages. [Read More]

In Uppsala I spent several months investigating the generation of displacement fields with known volume changes, and I even implemented a software suite for the purpose. This might seem an odd topic to pick as working subject, so it is worth a bit of clarification about its purpose and applications.... [Read More]

This post is meant to be a brief introduction to some productivity tools that can make a command line workflow smoother and more efficient. While well known, standard tools with similar function already exist (e.g. bash, grep, find, etc.), the tools presented hereafter have a handy user interface with sensible... [Read More]

Currently, I work mostly on image registration algorithms, and I devoted quite some time looking into groupwise registration techniques. In its essence, groupwise registration is a process that aligns multiple images, mapping them to a common reference space, without having to explicitly define such reference space (e.g. without manually selecting... [Read More]

Visualisation is a complementary but very important part of my work on image analysis. And since I work mainly with tridimensional volume images, visualisation is inherently a more complicated task compared to image analysis in only two dimensions. To help my work, I decided to implement a small tool for... [Read More]

Python is a high-level programming language whose extremely simple and elegant yet very powerful and expressive syntax has granted it enormous popularity in most programming contexts. Scientific applications are no exception on this respect, and this may look strange at a first glance, given that Python’s runtime is painfully slow... [Read More]