## In Circles: fitting a circle to a curve

A comment from a referee led me to find a method to describe curvature of membranes. This is a quick write-up of our solution. I couldn’t find a solution readily available in Fiji, so I created one using a combination of Fiji for tracing the curvature and IgorPro to do the fitting. If there is […]

## Line Up: Waffle plots for colocalisation data

Quantifying the degree of colocalisation of two signals in microscopy images is very tricky. Lots has been written on this topic, including in my book The Digital Cell. The focus of this post is on visualising colocalisation. One way to look at colocalisation is two think about two sets of objects and how many of […]

## Seles: Tennis coding challenge

A colleague sent me a coding challenge. This is a short post to describe how I tackled it. Edit: a follow-up post is here. This is the challenge: There is a tennis match between two players denoted 1, and 2. You are given a sequence of 1s and 2s whereby each number denotes a point […]

## Walk This Way

Over the holidays, I had an idea about looping an animation between two images. I wrote some code to do this in Igor Pro (sorry, no R this time…). This post describes how the code works and how you can make a similar animation. There was a reason to do this animation, but as a […]

## Rotation: using quaternions in Igor Pro

Quaternions are essentially magic. With just four numbers, they can describe the position and orientation of an object in space. For example, the rotation of an object about one axis. Consecutive rotations can also be described by a quaternion. There are many explainer articles which help to understand quaternions and their uses (they are used […]

## Turn A Square: generative aRt

A while back I visited Artistes & Robots in Paris. Part of the exhibition was on the origins of computer-based art. Nowadays this is referred to as generative art, where computers generate artwork according to rules specified by the programmer. I wanted to emulate some of the early generative artwork I saw there, using R. Some […]

## Small Talk: How big is your lab?

I really dislike being asked “how big is your lab?”. The question usually arises at scientific meetings when you are chatting to someone during a break. Small talk can lead to some banal questions being asked, and that’s fine, but when this question is asked seriously, the person asking really just wants to compare themselves […]

## My Blank Pages VI: Programming in Igor Pro

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 […]

## Cloud Eleven: A cloud-based code sharing solution for IgorPro

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 […]

## Esoteric Circle

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 […]