The Process_Folder template in Fiji is a wonderful thing. It’s the starting point of most of the ImageJ macros that we use in the lab. However, it has a problem. This post is about how to fix it. tl;dr use this gist instead of the built-in template. The Process_Folder template If you’re reading this, you […]
Tag: ImageJ
Monster Movie: making movie files from microscopy data
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 […]
Point Me At The Sky: wall art using Raspberry Pi camera images
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 […]
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 […]
New Lexicon: how to add a custom minted lexer in Overleaf
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 […]
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 […]
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 […]