Director of Scientific Computing, Allen Institute for Neural Dynamics
Joined August 2017
- Tweets 401
- Following 130
- Followers 428
- Likes 578
73 Photos and videos
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
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David Feng retweeted
17 Jul 2023
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/s00418-023-0…
8 May 2023
#OMEZARR @biorxivpreprint v4 now available
with newly added teams incl. @CiminiLab @fabian_theis @imweio @loicaroyer @ngehlenborg @OliverStegle @sonamix & an apparently elusive Nathan Hotaling
❤️Love to see the growing list of resources, e.g. ngff.openmicroscopy.org/data…
ALT Screenshot of https://ngff.openmicroscopy.org/data/index.html showing a table of "Data Resources" along with where the catalog is hosted, how many Zarr filesets are published, and their estimated size in GB or TB.
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David Feng retweeted
12 Jun 2023
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/10.1101/…
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David Feng retweeted
5 Jun 2023
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/10.1101/…
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David Feng retweeted
9 Mar 2023
"Toward #scalable reuse of #vEM data: #OMEZarr to the rescue" just hit the shelves!📚
doi.org/10.1016/bs.mcb.2023.…
Special thanks to co-authors @normanrz & @BogovicJohn, co-artist @DrHenningFalk, and volume (ha!) editors @EM_STP @KedarNarayan2 & @PaulVerkade
ALT "Monolithic vs. chunked" by Henning Falk, ©2022 NumFOCUS, is used under a CC BY 4.0 license. Modifications to this photo include cropping. The image shows a three-by-three collection of cubes labelled, 000 through 0YX with arrows labelled "ACCESS" pointing at two chunks which are colored blue and red.
ALT Screenshot of section 7.3 "How many files will chunking create?" that outlines the number of files and size per file (in bytes) are required for a 4.4 trillion voxel image.
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David Feng retweeted
21 Feb 2023
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/10.1101/…
ALT Figure 1 of the paper showing 6 different modalities labeled (a) multiplexed imaging, (b) spatial transcriptomics, (c) light-sheet, (d) infrared, (e) scanning EM, and (f) digital pathology. Lines show how data flows into Converters which then can be stored either on remote or local scalable storage. This enables visualization tools or parallel processing.
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25 Oct 2022
I just learned the phrase "screaming snake case" and can't stop giggling.
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David Feng retweeted
11 Sep 2022
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?
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9 Sep 2022
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.
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5 Aug 2022
Quote of the day: "Just a quick heads up - I am going hunt you all down. For metadata."
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18 May 2022
More adventures in generative models. I threw pokemon at github.com/lucidrains/denois… without touching anything and the results are fun.
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18 May 2022
I switched the loss function from L1 to MSE and the style change is cool.
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David Feng retweeted
7 Apr 2022
We made our pre-beta version of light sheet based mouse P56 brain template with Allen CCF labels at 10μm isotropic resolution. Please DM me if you want to try it for your brain mapping. Happy to share in condition for user feedback :)
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1st Get Your Brain Straight Hackathon - bringing together🧠neuro data generators, 🛠️image registration experts and 💻compute infrastructure providers for a hands-on collaborative virtual event
April 4-7, 2022
#BICCN @AllenInstitute @Kitware #BrianImagingLibrary #StudyBRAIN
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David Feng retweeted
14 Mar 2022
I am looking for a research engineer to join me at the @AllenInstitute for Neural Dynamics. If you are (or know) a recent or soon to be graduate interested in working on next generation light-sheet software hardware please apply share! alleninstitute.hrmdirect.com…
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14 Feb 2022
Some scientists on the team are looking for instructional materials for data analysis in Python, many migrating from MATLAB with limited software experience. I have some old links kicking around, but would love to hear from y'all. What's the state of the art?
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David Feng retweeted
11 Jan 2022
We know that coding knowledge is useful in neuroscience research, but how do we train our students when few bio instructors are proficient in coding and C.S. classes are full? 🤔
I tackle these issues in this NeuroView for @NeuroCellPress!
authors.elsevier.com/a/1eOdV…
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5 Jan 2022
I thought Wordle made word/tag clouds. Sadly it's been discontinued and I feel just a little bit older now.
Wordle 200 4/6
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