I read about Antonio Sánchez Chinchón’s clever approach to use the Travelling Salesperson algorithm to generate some math-art in R. The follow up was even nicer in my opinion, Pencil Scribbles. The subject was Boris Karloff as the monster in Frankenstein. I was interested in running the code (available here and here), so I thought I’d run it on a famous scientist.

A few days ago, I read an article about Damien Hirst’s new spot paintings.

Many projects in the lab involve quantifying circular objects. Microtubules, vesicles and so on are approximately circular in cross section. This quick post is about how to find the diameter of these objects using a computer. So how do you measure the diameter of an object that is approximately circular? Well, if it was circular you would measure the distance from one edge to the other, crossing the centre of the object.

Another post using R and looking at Twitter data. As I was typing out a tweet, I had the feeling that my vocabulary is a bit limited. Papers I tweet about are either “great”, “awesome” or “interesting”. I wondered what my most frequently tweeted words are. Like the last post you can (probably) do what I’ll describe online somewhere, but why would you want to do that when you can DIY in R? First, I requested my tweets from Twitter.

To validate our analyses, I’ve been using randomisation to show that the results we see would not arise due to chance. For example, the location of pixels in an image can be randomised and the analysis rerun to see if – for example – there is still colocalisation. A recent task meant randomising live cell movies in the time dimension , where two channels were being correlated with one another.

I’ve generated a lot of code for IgorPro. Keeping track of it all has got easier since I started using GitHub – even so – I have found myself writing something only to discover that I had previously written the same thing. I was thinking that it would be good to make a list of all functions that I’ve written to locate long lost functions.

A large amount of time doing data analysis is the process of cleaning, importing, reorganising and generally not actually analysing data but getting it ready to analyse. I’ve been trying to get over the idea to non-coders in the group that strict naming conventions (for example) are important and very helpful to the poor person who has to deal with the data.

We have some macros for ImageJ/FIJI for making figures and blind analysis which could be useful to others. I made an ImageJ Update Site so that the latest versions can be pushed out to the people in the lab, but this also gives the opportunity to share our code with the world. Feel free to add the quantixed ImageJ update site to your ImageJ or FIJI installation. Details of how to do that are here.

This is part-tip, part-adventures in code. I found out recently that it is possible to comment out multiple lines of code in Igor and thought I’d put this tip up here.

A couple of recent projects have meant that I had to get to grips more seriously with R and with MATLAB . Regular readers will know that I am a die-hard IgorPro user. Trying to tackle a new IDE is a frustrating experience, as anyone who has tried to speak a foreign language will know. The speed with which you can do stuff (or get your point across) is very slow.