David Hoffman
@davephoffman
Sr. Staff Optical Engineer at @10xGenomics: 🔬+ 🧬. Views are my own (whose else’s would they be?)
Taking #CLEM into the 21st century, read all about it here science.sciencemag.org/content/367/64… watch all the videos here vimeo.com/showcase/66925… and extra points for anyone that even attempts to read the full supplement. Great #science when #biology and #physics meet
The nd2 package (Nikon NIS elements file reader for python) just got a major internal refactor. v0.6.0 reimplements the outputs of the official SDK in pure python. (No more wrapping of c code) Speed is improved, and it’s easier to install anywhere now. github.com/tlambert03/nd2
Correlative two color 3D super-resolution single molecule localization microscopy and block face electron microscopy of mitochondria and the endoplasmic reticulum in vitreously frozen COS-7 cells doi.org/10.1126/scienc…
(1/x) We are excited to introduce VIPS (Volumetric Imaging of biological specimens via Photochemical Sectioning) in our preprint! VIPS uses a light-based process called “photochemical sectioning” to achieve petabyte-scale high/super-resolution imaging: biorxiv.org/content/10.110…
We're very pleased to announce the February issue of Nature Methods, which includes a "mini-Focus" follow-up to our July 2023 Focus Issue on the future of bioimage analysis! (please see thread) nature.com/nmeth/volumes/…
✅💡 very happy to have this paper finally out. Chris and I started working on this project in 2017…so great to get this across the line at last! nature.com/articles/s4158…
🔬🚨 New preprint from @cjobara and myself during our time together in the @JLS_Lab and Blackstone lab. Motion of single molecular tethers reveals dynamic subdomains at ER-Mito contact sites...a (belated) thread🧵...(1/9)
Cellular organelles exchange molecular information through transient contact sites, which are sensitive to experimental analysis. Reporting @nature, scientists use advanced microscopy to map and analyse dynamic subdomains at ER-mitochondria contact sites. shorturl.at/jAX39
Nature research paper: Motion of VAPB molecules reveals ER–mitochondria contact site subdomains go.nature.com/4bcisy8
Excited to share our comparison of Xenium and CosMx data! I feel like a lot of labs/core facilities have made similar observations internally, so we're really glad to put this out for the broader community. biorxiv.org/content/10.110… 1/n
I’m going to quietly leave this here…but not without a shoutout to @DavidPCook, @kirkbjensen and @Kellieiswise for their AMAZING work. 🙌 A Comparative Analysis of Imaging-Based Spatial Transcriptomics Platforms biorxiv.org/content/10.110…
Muyuan has been working on this for some time, it's cool to see a manuscript: How to create full, atomic resolution scenes of biomolecules in Unreal Engine and fly around them in real-time. Really cool stuff with untapped potential. eman2.org/unreal_render biorxiv.org/content/10.110…
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Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues biorxiv.org/cgi/content/sh… #biorxiv_cancer
My favorite dataset thus far. Just an entire mouse pup in a single run. NBD
Biology is beautiful—and Xenium proves it by bringing it to life with the new Mouse Tissue Atlasing Panel. Learn how #singlecellspatial imaging can help you uncover the splendor of your sample here: bit.ly/4835hhy
If you are imaging more than one fluorophore in your specimen, be sure to perform the correct controls to ensure your results are not confounded by bleedthrough or autofluorescence! youtu.be/D_vxHMWC2mQ
What if you could explore 1,000s of your genes at subcellular resolution & get deeper cellular and spatial insights? What if you could do it with near-instant data after a run? Don’t wonder: find out how Xenium can take your ‘what ifs’ to ‘what next’. 10xgen.com/47blS2g
Our paper on fluorescence lifetime voltage imaging of neurons is out! We combine kilohertz frame rate, micrometer spatial scale, and picosecond lifetime resolution in vivo. Check out the videos and original thread below. @ChengHuangThu science.org/doi/10.1126/sc…
🎉 Guess what just landed? More #spatial omic fun is here!!! @10xGenomics
Image provided by @10xGenomics of a whole mouse pup run using the #Xenium Mouse Tissue Atlassing panel! 🧬👏
If you like building cool light-sheet microscopes, this is for you. The benchtop mesoSPIM @MesoSpim is faster, has better optics, larger field of view. Works for whole mouse, human cortex and more. @voigtvision @FritjofHelmchen @nvladimus biorxiv.org/content/10.110…
If you currently own or have ordered a CosMx, we want to help keep your science moving forward. We are offering special promotions to help you transition to Xenium. Learn more: 10xgen.com/41OTXkG (5/5)
I recently drew an a piece that shows the molecules found in whiskey. Vanillin, eugenol, and many other compounds give whiskey its unique flavor profile. Cheers to whiskey! 🥃 #ChemTwitter