Posts about image processing of microscopy images usually using the open source software ImageJ/Fiji.
The Light-Sheet Image Analysis Workshop organized by LiSIUM took place last week at Universidad Mayor in Santiago, Chile. There were 24 participants from all over Latin America—Argentina, Brazil, Chile, Colombia, Mexico, and Uruguay! Marina Cuenca, Agustin Corbat, and I (the instructors) gave lectures and practicals ranging from the basics of digital images to advanced workflows […]
The Light-Sheet Image Analysis Workshop is a five-day intensive course that will take place in Santiago, Chile, from January 5–9, 2026, designed for students and researchers who wish to gain foundational skills in the processing and analysis of light-sheet microscopy imaging data. The application deadline has been extended until August 8, 2025! The workshop is […]
In a recent email exchange, someone asked me what the colors in the video of mitotic waves mean and how did I get them. How the microscope technique results in the array of colors in the cells (purple to yellow and red). Could you briefly explain where the colors come from and how you visualised […]
I’m refactoring the image processing functions of the Cifonauta database and wondering if there’s any Python library with native video processing capabilities. For the past years, I used a subprocess.call() to run a FFmpeg command to scale down and convert video files for the Cifonauta website (which is Django-powered). The ffmpeg command has some niceties […]
After posting the first version of our cephalic furrow pre-print, I received an email asking for further technical details about using the CARE upsampling module to restore the Z-resolution of lightsheet datasets: I am curious about some details of your “Pre-patterned epithelial invagination prevents mechanical instability during fly gastrulation” paper. You mention that you trained […]
Note: The denoising I describe in this post was done for artistic reasons and not for scientific purposes. For the proper methodology on image denoising, please follow the CARE paper. I wanted to denoise a twenty-year-old photomicrograph. It’s one of the first scientific images I created back in 2003. It’s so ancient that I used […]
When I film embryos under the microscope, some will be younger and some will be older than others—they are never in perfect synchrony. This is fine when watching the recordings of individual embryos, but becomes an issue when you want to watch two (or more) embryos developing side-by-side. In my case, I want to identify […]
This is a bryozoan embryo with its blastopore facing us. The blastopore is the hole in the middle. The “balls” are the nuclei of the cells that make up the embryo. While cells have many other structures, they are not visible in this image. The only thing visible is the DNA because I stained it […]
Something I’m doing more often is converting videos of developing embryos or marine invertebrates to animated GIFs. But how can you do this conversion without affecting the quality of the video? Some time ago I found this guide to convert videos to high-quality animated GIFs using the tool FFmpeg. The trick is to generate a […]
A short video that I made about the embryonic development of the likeable Drosophila, also known as fruit fly or vinegar fly, won an honorable mention in the Small World in Motion. The details on the techniques I used and the video on its full resolution are available for download and re-use on the Wikimedia […]