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biology articles code imaging

Improving Z-resolution of lightsheet data using CARE upsampling

After I posted the first version of our cephalic furrow pre-print, I got the following email asking for technical details about using CARE upsampling 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 a […]

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biology articles imaging

Denoising an old photomicrograph

Note: The denoising I describe in this post was not done for scientific purposes, but for artistic reasons. For proper methods on image denoising, follow the CARE paper trail. 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 a […]

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imaging articles code

ImageJ macro to synchronize and combine image stacks

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 […]

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biology imaging notes

The blastopore of bryozoan embryos

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 […]

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articles code

Convert video to animated GIF

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 […]

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biology imaging notes

Fruit fly embryo under lightsheet microscopy

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 […]