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! 📝
https://t.co/iSFOr3RYYU
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
https://t.co/Kl7ZURNpdM
🧵 (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.
https://t.co/sH1Lt5k3Xw
(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.
@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!
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.