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Adding ManyToManyField values to SearchVectorField for full-text search in Django

Summary Get the related values joined in a string and pass it on as a Value() expression in the SearchVector object: Cifonauta’s full-text search During the past year, we’ve been working on several updates for modernizing the Cifonauta database. The website now has a fully responsive design and a new dashboard for contributed user uploads. […]

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EvoDevo Papers, refactored

EvoDevo Papers is a bot that shares research articles in the field of evolutionary developmental biology (or evo-devo). Originally, I created it as a Twitter bot and everything was going well for years… until Twitter’s takeover. The new policies and API restrictions made it unsustainable to continue posting there. In response to that, I decided […]

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Native video processing in Python

I’m refactoring the image processing functions of the Cifonauta database and wondering if there’s any Python library with native video processing capabilities. For the past years, I used a subprocess.call() to run a FFmpeg command to scale down and convert video files for the Cifonauta website (which is Django-powered). The ffmpeg command has some niceties […]

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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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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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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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Convert notes from Simplenote to Zim Desktop Wiki

Zim Desktop Wiki is my primary note-making software. I use it to take notes, organize my projects, manage daily and long-term tasks, grow a digital garden, keep a journal, and more. Zim is great for the desktop, but it lacks a mobile app. So I’ve been using Simplenote for saving notes on the go. The […]

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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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Winter Wandering

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InverteFest December 2022

The InverteFest is here. A moment to celebrate the overlooked diversity of invertebrates around us. I’m re-posting a video I made for the Cifonauta account on Instagram showing different marine invertebrates moving around under the microscope. Enjoy! Invertebrate Gallery Check the gallery below to find out the identity of each marine invertebrate in the movie […]