Moving the blog

I moved my blog! Not just in terms of where it’s hosted, but how the whole thing is built. Previously I’d been using ghost, which was fine up until the moment I wanted to publish more code/analysis. The process of copy-pasting code and exporting images was taking more time than writing the code itself. I’m now using the blogdown package which builds static websites within RStudio using Hugo and lets you publish the results.

Continue reading

I have a bit of a love hate relationship with kymographs. In the way that they compress data there’s no doubt that you loose information, but in the world of axonal transport and low signal:noise they have clear advantages in enabling quantification. I covered before a couple of strategies you can use to import image data into R. The next step in my workflow is usually to turn that image into a data table for further analysis.

Continue reading

Andreas Prokop raised the issue of kinesin nomenclature on twitter over the weekend “I am tired of having to look up lists!”. I couldn’t agree more, it’s insanely confusing - especially when you’re trying to synthesise literature across several model organisms (shout out to Ustilago maydis and Dictyostelium discoideum here). Why is it confusing? The standardised kinesin nomenclature was defined in 2004, where the superfamily was divided into sub families. They even defined how motors should be referred to in the text.

Continue reading

The science twitter community can be a hugely beneficial resource, it can also be overwhelming if your new to it. I asked the scientists of twitter what platform they were using to interact with twitter itself (‘for a thing’). This post is not the thing I was eluding too, but the poll threw up a few tips I thought it worth drawing attention too and I figured I’d chuck some of my own tips in while I was at it.

Continue reading

Importing images into R

In May my paper was finally released into the wild. Amongst other things it was the culmination of 4 years of me learning to use R for data analysis (and in my case data = images of cells). I’ve been meaning to blog some of this for a while, but I will try for my own sanity to keep everything in bite size chunks. Starting at the start: data import.

Continue reading

Merry Christmas!

When I was on the microscope imaging EB3 comets in axons as a control experiment for a control experiment, I got distracted by the comets in the dendrites - so pretty! They reminded me of the icicle lights on the outside of people’s houses you see this time of year. So this is my science Christmas card to you - have a Merry one :)

Continue reading

Author's picture

Ali Twelvetrees

Research scientist looking at kinesin, dynein and neurons; trying to figure out how stuff moves around inside neurons and how it goes wrong in neurodegeneration.

Vice Chancellor’s Fellow