David Feng

Sharing🤯video to get you through Friday! Credit: @E_cross_B @Blender animation of the Allen Mouse Common Coordinate Framework (#CCF). Outer structures "explodes" out to reveal inner brain structures. @AllenInstitute

Out now! "#OMEZarr: a #CloudOptimized #BioImaging #FileFormat with Int'l #Community Support" 😍 Huge thanks to the 68 co-authors, across 32 institutions (see the quoted tweet) 🙌 If you use #OMEZarr & weren't involved, let's start the next report! 📝 doi.org/10.1007/s00418…

@adam_k_glaser Congrats @adam_k_glaser and team! Some of the most beautiful (and largest!) data I have ever seen 🤩

How do you image the large and the small at the same time? We developed new 🔬 technology to image centimeter-scale specimens - including whole mouse brains 🧠 - with diffraction-limited resolution and without sectioning. #mesoscale #imaging biorxiv.org/content/10.110… 🧵 (1/n)

@BWJones @grimmrad @RetoPaul We usually do one Zarr "file" per acquisition session -tend not to need to update/rebuild anything. Although I feel like I may be misunderstanding.

Do you use #neuropixels or #highdensity probes? Are your recordings filling up your hard drives? We got you covered! In the first preprint from @AllenInstitute for Neural Dynamics, we looked at ways to reduce the footprint of #ephys data. biorxiv.org/content/10.110… (1/n)

@buccino_alessio @AllenInstitute Congrats @buccino_alessio and team! Effective data compression is often treated as an afterthought, but long term it saves everyone time and $$$. Hopefully everyone else can take advantage of this as well!

@grimmrad @BWJones @RetoPaul We like OME-Zarr for this. Zarr comes with a whole bunch of lossless codecs that are trivial to apply. For our SPIM data we routinely get 5-8X lossless compression.

"Toward #scalable reuse of #vEM data: #OMEZarr to the rescue" just hit the shelves!📚 doi.org/10.1016/bs.mcb… Special thanks to co-authors @normanrz & @BogovicJohn, co-artist @DrHenningFalk, and volume (ha!) editors @EM_STP @KedarNarayan2 & @PaulVerkade

Latest report from the #OMENGFF #Community describing #OMEZARR, a #CloudOptimized #BioImaging #DataFormat, is out now on #bioRxiv! If you have issues with big, slow, or otherwise unwieldy imaging data, reach out or take a look for a #FAIR-er option. biorxiv.org/content/10.110…

@_martinthoma erdantic.drivendata.org/stable/

Is there a library/script to visualize a #pydantic model as a class diagram?

@neuromusic ding ding

@dyfbrain SCREAMING_SNAKE_CASE <- ?

I just learned the phrase "screaming snake case" and can't stop giggling.

@chrhagel As with most things, it's funnier without the explanation: dev.to/fission/scream…

@dyfbrain What is screaming snake case? Spread the giggles.

@neuromusic @jedsundwall twitter.com/dyfbrain/statu…

@jedsundwall CC0 licensed of course 😁

Nah, it just ended up not being as magical as advertised. “Open data” has been a mostly useless conceptual frame. “Open” isn’t a category of data. *Openness* is an attribute of data products, and it depends on various things like license, ease of access, byte volume, etc.

@adam_k_glaser @AllenInstitute @MesoSpim Maybe next time I will keep my big mouth shut when I tell an acquisition team to "just collect better data." This data is huge!

A sneak peak into our molecular anatomy lab and light-sheet work at the @AllenInstitute for Neural Dynamics for #OpenScienceWeek! Great to see Xiaoyun and Joshua working with their modified @MesoSpim. Excited to share our other custom light-sheet builds that are in progress soon!

What do scientists here use to keep track of experiments, subjects, local datasets, etc? Spreadsheets, Airtable, structured SQL databases? MongoDB or Firebase? Some special software because of PII or HIPAA? What has worked for you in the past, and what hasn't?

Quote of the day (~5 years ago): "You're just secretly trying to convert all of our scientists to software engineers, aren't you?" Here's to hoping it's now safe to set aside my secret devops agenda.

Quote of the day: "Just a quick heads up - I am going hunt you all down. For metadata."

Surrealist pokemon, so fun.

I switched the loss function from L1 to MSE and the style change is cool.

More adventures in generative models. I threw pokemon at github.com/lucidrains/den… without touching anything and the results are fun.