As part of my PhD project, I have been writing a program in C++ to track hundreds of bees that I have tagged and to identify the pattern on the tags. Initially, I had thought that recognising the tags would be rather simplistic – I could threshold out the tags that are reflective under IR …

Recently I used the program FFmpeg to automatically extract metadata about the time and date some videos I’ve been using for my research were created. FFmpeg is a really useful tool for manipulating videos and images at the command-line. You can do things like change the format, quality or length of your video files with relative …

I have a talk today about how I’ve been using the iPython Notebook when prototyping different image processing techniques and their parameters. The presentation involved a bit of background on how to use the notebook and markdown, before I demonstrated how you could use the notebook to rapidly test out the best way to process …

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The project I am working on at present is focused on building an automated system for tracking the movement of honeybees in an observation hive, filmed using a grayscale camera and infrared light. My recent attempt at this has involved extracting features (or keypoints) from the frames and then describing them using the SIFT (Scale Invariant …

I commenced my PhD in bioinformatics at the Australian National University about a month ago and thought I’d share some of the tools I’ve found absolutely essential. All of these tools are free to use (some do have paid plans, however at this point I haven’t had the need to sign up for them). Evernote + …

This tutorial is a brief overview of what you can achieve using the Python BioPython module. Although I’m hoping to write up some more articles on this site for beginners when time permits, this post will assume that you have experience programming in Python and have a bit of an understanding of basic biological concepts …

Pyral (Python + Viral) was the name of a project I worked on in Dr Joanne Macdonald’s lab between September 2012 – January 2013 (although I am still providing tech support for the code and helping manage the server to this date). Throughout this time I wrote a lot of Perl and Python code to run …