Bees, lasers, and machine learning

I originally wrote this article about how I’ve used machine learning as part of my research for the Data Skeptic blog. If you’re interested in machine learning, I can’t recommend their podcast enough. A couple of years ago I started my PhD at the Australian National University working to quantify honeybee behaviour. We wanted to …

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Why I post my writing to Reddit

Recently, I helped establish BioSky – a website dedicated to making medical and health research accessible to people without a scientific background. As we’ve been adding content to the site, I’ve been posting the links to multiple social networks including Facebook, Twitter, LinkedIn and Reddit. If I had to pick only one platform to use, it would …

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Announcing BioSky

BioSky is a website I’ve been setting up with Rina Soetanto recently. We are both doing PhDs in the biological sciences and have a keen interest in research and the treatments being developed in the biotech and health industry.

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Compiling C++ Code Using Caffe

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 …

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Be careful with FFmpeg metadata

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 …

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iPython Notebook Presentation

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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Interesting Articles on Programming, Organisation and Bioinformatics

Programming Programming without For loops 9 Anti-Patterns Every Programmer Should Be Aware Of The Key To Accelerating Your Coding Skills 10 Python Machine Learning Projects on GitHub Organisation The Weekly Review: How One Hour Can Save You A Week’s Worth Of Hassle How to be the most productive person in your office — and still …

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Tracking bees using local features

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 …

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Essential Free Tools for Research

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 + …

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BioPython Tutorial

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 …

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