What’s the best way to make a movie file from microscopy data? Maybe you need to generate a movie for the supplementary info for a paper, or insert one into your electronic lab notebook, or to show in a talk. The problem is that the requirements for each of those is different. This situation is compounded by the fact that there are so many options to make movie files and not much guidance on what is the best method.

I have a long-running Raspberry Pi camera project to capture images of the view from a window (more details here). A recent post on mastodon, which showed a keogram, encouraged me to take my PiCam images and turn them into art. The finished product This is the finished wall art, printed on canvas. Ready to hang on the wall.

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 any interest I can convert this code into an all-Fiji routine. The code is simple and a gist is available here.

When preparing images for publication, it is good practice to check how accessible they are for colour blind people. Using a simple bit of code, it is possible to check an image – or a whole figure – in ImageJ for accessibility. For example, Figure 1 from our recent paper. Originally looked like this: Using the script we can see how it appears to people with different types of colour blindness.

Here is a fun post about using colour palettes in R. It starts with a computer game… After a few years of sporadically playing Super Mario World 2 – Yoshi’s Island on the Retropie, I made it to the final level.

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 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.

Molecular Biology of The Cell , the official journal of the American Society for Cell Biology, recently joined a number of other periodicals in issuing guidelines for manuscripts, concerning statistics and reproducibility.

Something that has driven me nuts for a while is the bug in FIJI/ImageJ when making montages of image stacks. This post is about a solution to this problem. What’s a montage? You have a stack of images and you want to array them in m rows by n columns. This is useful for showing a gallery of each frame in a movie or to separate the channels in a multichannel image.