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biology articles code imaging

Improving Z-resolution of lightsheet data using CARE upsampling

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 […]

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biology articles imaging music science

A Sea Biscuit’s Life turns fifteen

When I was finishing my master’s thesis, I created a video to summarize my findings and posted it online. I wanted to share the wonderful things I saw under the microscope—cells dividing, tissues folding, embryos spinning, larvae metamorphosing, juveniles crawling between sand grains. But I also wanted to convey the thrill I felt, seeing these […]

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biology articles imaging

Denoising an old photomicrograph

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 […]

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notes biology

Biology is exciting and informative

Biology is exciting and informative, giving us insight into the beauty of life. What we see with the microscope is the amazing developmental process by which form emerges out of unformed material. To watch an embryo develop is to see the life of a new individual emerge, gradually, stage by stage, from very simple material […]

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notes science

Introduction to Science Mastodon

After a first try back in 2020, I’ve recently migrated my account to my new social handle (@bruvellu) and started using Mastodon again. I’m excited about it. Migrating away from Twitter (and other corporate social silos) will be good for the web in general and for science communities in particular. Here’s my introduction to the […]

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biology articles imaging

Mitotic waves and gastrulation in a fly embryo

Last year I published a snapshot of a mitotic wave in a fruit fly embryo. Here’s the video of that same embryo going through cleavage (nuclei divisions) and gastrulation (cell movements): Mitotic waves What you see at the beginning of the movie are the cycles of synchronous nuclei divisions. They happen in waves from the […]

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notes biology imaging science

Sea biscuits on Labocine

I’m pleased to announce that my short video A Sea Biscuit’s Life is now available on Labocine at https://www.labocine.com/films/a-sea-biscuits-life. The sea biscuits are joining the Science New Wave!

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notes biology imaging

Brachiopod larva in the Nikon Small World 2021

This image of a brachiopod larva was selected in the Nikon Small World 2021 photomicrography competition!

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imaging biology notes

A mitotic wave

A mitotic wave traveling through an early #Drosophila #embryo #FlyFriday

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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 […]