Categories
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 🌈🔬

Categories
notes science

The boring parts of science

Science is exciting, right? You explore, you experiment, you make discoveries. You see things for the first time! Science is fun. But, it also has its boring parts. Today, for example, I spent four hours pipetting, non-stop. 280 tubes. No robots, no multichannel pipette. Just manual labor. The pipetting marathon is for an experiment, which […]

Categories
biology notes science

Visualizing gene expression over developmental time

Visualizing the dynamics of gene expression patterns over time is a challenge. But this is a nice way.

Categories
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 […]

Categories
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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notes code

Reply by Email

Blog posts are an invitation to interact. This usually happens in the comments section down below. But, posting public comments isn’t for everyone and it’s not the best option for every type of conversation. Often, a more direct and private response works better. As an alternative to regular comments, I added a reply by email […]

Categories
notes biology

Goldfish evo-devo

Kinya Ota’s Lab investigates the embryonic development and evolutionary biology of goldfish. Their YouTube channel has a great diversity of videos describing laboratory techniques, culture conditions, developmental time lapses, and a lot more. I’ve seen a few videos about fertilization and embryos, but I just found out that they’re doing a series on goldfish evo-devo! […]

Categories
notes biology science

Cephalic furrow preLights

preLights is a (another) great initiative from The Company of Biologists where teams of scientists review and comment on preprints of interest for the biology community. I was delighted to hear that they were going to highlight our cephalic furrow preprint (Vellutini et al.) combined with the cephalic furrow preprint of Lemke and Wang labs […]

Categories
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 […]

Categories
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 […]