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notes imaging science

Confocal excitation

The pipetting marathon I went through the other day was worth it—the experiment worked! Now I get to image some exciting and colorful samples in the confocal microscope, and experience that thrill of seeing something for the first time, once again 🌈🔬

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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

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 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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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!

Categories
imaging biology notes

A mitotic wave

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