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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

Cephalic furrow thread

I published a cephalic furrow thread about our paper on Twitter and Mastodon. We recently updated the manuscript on bioRxiv. In addition to the tissue mechanics, this new version includes gene expression data comparing Drosophila with Clogmia, a fly that has no cephalic furrow… It gives us some hints about the patterning changes associated with […]

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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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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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science articles imaging

The Science New Wave

The Science New Wave is a movement to reimagine science in the cinema. Its manifesto states: Culture is Science. Science is Culture.Diversity Feeds The Ecosystem.Experiments Become Cinema.Structure Dictates Function.Science & Story Never Collide.We are all messengers. Traits from the Science New Wave manifesto. I learned about the Science New Wave from Alexis Gambis, a biologist […]

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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 […]

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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 […]