@dyfbrain

Director of Scientific Computing, Allen Institute for Neural Dynamics

Joined August 2017
  • Tweets401
  • Following130
  • Followers426
73Media
David Feng retweeted
Lydia Ng@2queues6 Sep 2024
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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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…

OME-Zarr: a cloud-optimized bioimaging file format with international community support

Histochemistry and Cell Biology - A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the...

link.springer.com
Josh Moore@notjustmoore8 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…
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.

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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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/… 🧵 (1/n)
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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/… (1/n)
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"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
"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 "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.

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.

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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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/…
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.

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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I just learned the phrase "screaming snake case" and can't stop giggling.
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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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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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Quote of the day: "Just a quick heads up - I am going hunt you all down. For metadata."
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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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I switched the loss function from L1 to MSE and the style change is cool.
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Surrealist pokemon, so fun.
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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David Feng retweeted
Lydia Ng@2queues19 Mar 2022
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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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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David Feng retweeted
Randall Munroe
@xkcd17 Feb 2022
Data Trap xkcd.com/2582
Comic

ALT Comic

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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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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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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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