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biology articles code science

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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notes code

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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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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articles code

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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biology articles code

Living Bibliography

Living Bibliography was born when, a few weeks ago, on a Saturday morning, I bumped into the Hack4Knowledge, a meeting to build apps, tools, and remixes with existing databases to innovate and enrich the creation and dissemination of knowledge. I was already playing with the Mendeley API and took the opportunity to put an idea […]