ImageJ is the open-source image processing and analysis software, and Fiji Is Just ImageJ with batteries included.
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 […]
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 brachiopod embryo at the gastrula stage, showing its outer surface and the blastopore at the bottom. To visualize the cell membranes, I stained the sample for F-actin (filamentous protein fibers present in cells) and acquired a volumetric image stack in a confocal microscope. Then, I converted the original data to a 3D […]