This quick post comes courtesy of LianTze Lim (an Overleaf TeXpert) and Kota Miura (a bioimage analyst). I asked on the ImageJ forum some time ago how to add an ImageJ Macro lexer for a LaTeX document I was writing. Kota responded with this lexer for pygments. I then asked Overleaf if it was possible to add a custom lexer to an Overleaf document using the minted package. At the time this was not possible.

The Green Leek 10.5 km run is a mixed terrain race now in its third year. Today’s was a wet and muddy edition. The chip times were posted this afternoon and using my previous code, I took a look at the results. I was a bit disappointed with my time, which was about 24 s slower than last year. Considering that I’m running faster this year than last, I wondered whether the conditions affected my time.

I’d seen the small multiple artwork of running and cycling routes from Marcus Volz’s R package Strava all over the web. Ads for “posters of your GPS tracks” pop up on Reddit and I’d notice a few #Rstats people put up their posters on Twitter. I’ve had the package bookmarked for a while and this week I finally got round to generating a small multiple poster of some of my cycling routes.

It has been a long time since I wrote a book review. A few months ago I read on IgorExchange that Martin Schmid had written a book about programming Igor. I snapped up a copy. I’m a competent Igor programmer but I was hoping that this book would be useful for lab members that want to learn. Learning Igor – like most IDEs or programming languages – is tough going.

I’ve previously crunched times for local Half and Full Marathons here on quantixed . Last weekend was the Kenilworth Half Marathon (2018) over a new course. I thought I’d have a look at the distributions of times and paces of the runners. The times are available here. If the Time and Category for finishers are saved as a csv, the script below works to generate the following plots. Aggregated stats for the race are here.

Some great scientific data gets posted on Twitter. Sometimes I want to take a closer look and this post describes a strategy to do so. Edit: I received a request to take down the 3D volume images derived from the example dataset I used in this post. I’ve edited the post below so that is now a general guide. Grab the video It can be a bit difficult to the grab video from Twitter. The best way I’ve found is using youtube-dl.

We have a new paper out. It’s not exactly news, because the paper has been up on bioRxiv since December 2016 and hasn’t changed too much. All of the work was done by Nick Clarke when he was a PhD student in the lab. This post is to explain our new paper to a general audience.

This post has been in my drafts folder for a while. With the World Cup here, it’s time to post it! It’s a rule that a 3D assembly of hexagons must have at least twelve pentagons in order to be a closed polyhedral shape. This post takes a look at why this is true. First, some examples from nature. The stinkhorn fungus Clathrus ruber , has a largely hexagonal layout, with pentagons inserted.

In a previous post I made a little R script to crunch Google Scholar data for a given scientist. The graphics were done in base R and looked a bit ropey. I thought I’d give the code a spring clean – it’s available here. The script is called ggScholar.R (rather than gScholar.R). Feel free to run it and raise an issue or leave a comment if you have some ideas.

There have been several posts on this site about publication lag times. You can read them here. Lag times are the delays in the dissemination of scientific data introduced by the process of publishing the paper in a journal. Nowadays, your paper can be online in a few hours using a preprint server. However, this work is not peer reviewed. Journals organise a formal peer review and provide some sort of certification of the work.

This post is something of a “how to” guide. The problem is how can you share code with a small team and keep it up-to-date? For ImageJ, the solution is simple. You can make an ImageJ update site and then push any updated code to the user when they startup ImageJ. For IgorPro, there is no equivalent. Typically I send ipf files to someone and they run the code, but I have to resend them whenever there’s an update.