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 […]
Tag: FIJI
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 […]
Colorblind: Checking figure accessibility for colour blind people
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 […]
Color Bars
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. In the background, as Bowser approached, I noticed that those coloured bars in the […]
Rip It Up: Grabbing movies from Twitter for use in ImageJ
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 […]
Adventures in Code III: the quantixed ImageJ Update site
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 […]
Tips from the blog X: multi-line commenting in Igor
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. Multi-line commenting in programming is useful two reasons: writing comments (instructions, guidance) that last more than one line the ability to temporarily remove a […]
Blind To The Truth
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. I discussed these guidelines with the lab and we felt that there are two areas where we can improve: blind analysis power calculations A post about power […]
Everything In Its Right Place
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 […]
Tips from the blog VII: Recolour Z-stack and Save Projection
I’m putting this up here in case it is useful for somebody. We capture Z-stacks on a Perkin Elmer Spinning Disk microscope system. I wanted to turn each stack into a single image so that we could quickly compare them. This simple macro does the job. We import the images straight from the *.mvd2 library using […]