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Doug Shepherd

@dpshepherd.bsky.social
614 followers 416 following 51 posts

recovering alpinist and scientist.

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Doug Shepherd @dpshepherd.bsky.social · 10/12/2025
We're still exploring how to improve LSFM performance with "big" detection air objectives, where field curvature often limits achievable FOV. Here, Steven introduces curvedASLM, a method to dynamically correct field curvature (along one axis) in axially scanned setups www.biorxiv.org/content/10.6...
Schematic on how to correct field curvature along light-sheet propagation axis.
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Doug Shepherd @dpshepherd.bsky.social · 14/11/2025
If you've seen anyone from the lab talk about RNA-FISH over the past years, they've shown data somehow related to this preprint. After a wandering road writing it up, happy to put out some thoughts on scalable 3D imaging-based spatial transcriptomics data processing. www.biorxiv.org/content/10.1...
biorxiv.org
GPU-accelerated, self-optimizing processing for 3D multiplexed iterative RNA-FISH experiments
Imaging-based spatial transcriptomic approaches rely on iterative labeling and imaging of carefully prepared samples, followed by solving a computational inverse problem to determine the location and ...
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Doug Shepherd @dpshepherd.bsky.social · 06/11/2025
We are really enjoying having Nick Galati visit us on sabbatical for some fun protist work, including our first forays into expansion microscopy! Max projection xy&xz views of expanded paramecium and tetrahymena cells. Scale bar is ~5.5 um accounting for expansion. Epifluorescence + deconvolution.
Pseudo-colored fluorescence microscopy image of expanded paramecium and tetrahymena cells.
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Reposted by Doug Shepherd
Alexa Mattheyses @mattheyseslab.bsky.social · 27/10/2025
🔬We are now accepting applications for the 2026 Analytical and Quantitative Light Microscopy course at MBL. Come learn to be an excellent microscopist! Questions? Ask here or DM me. @mblscience.bsky.social @aqlm.bsky.social #microscopy #fluorescence
Microscope built on rails
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Reposted by Doug Shepherd
Smitha Maretvadakethope (she/her) @mathsmaret.bsky.social · 11/09/2025
Our special issue of Phil Trans Roy Soc A on "Biological Fluid Dynamics" Emerging Directions" is officially out now! Originating from discussions at one of our SIG meetings, this special issue has 16 research articles and reviews on all things bioactive! royalsocietypublishing.org/toc/rsta/202...
royalsocietypublishing.org
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences: Vol 383, No 2304
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Doug Shepherd @dpshepherd.bsky.social · 13/08/2025
@ptbrown1729.bsky.social and the rest of the team's work on high-speed optical diffraction tomography plus structured illumination microscopy is finally out! www.science.org/doi/10.1126/...
science.org
Fourier synthesis optical diffraction tomography for kilohertz rate volumetric imaging
Highly multiplexed diffraction tomography enables kilohertz volume imaging for dynamic soft matter and biological systems.
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Doug Shepherd @dpshepherd.bsky.social · 04/06/2025
Spending some time at #lsfm25 cleaning up code. It now has distributed GPU gradient-consensus RL decon (@jamesdmanton.bsky.social @andrewgyork.bsky.social) our fast orthogonal deskew, and stitching/fusion to ome-ngff v0.5. Example AO-OPM data on uncleared mouse brain slice github.com/QI2lab/opm-p...
Adaptive optics oblique plane microscopy of 100 um thick mouse brain slice with immunofluorescence.
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Doug Shepherd @dpshepherd.bsky.social · 09/04/2025
Steven has our Snouty-OPM running again after our lab move. He added projection mode, sensorless AO, and a new control GUI based on @talley.codes + crew's pymmcore-plus/pymmcore-gui. Here are some IF-labeled microglia (orange) in the middle of an uncleared 60um mouse brain slice. No deconvolution!
Immunofluorescence image of a mouse brain slice, with nuclei (magenta) and microglia (orange) shown.Zoomed in Immunofluorescence image from the full mouse brain slice, with nuclei (magenta) and microglia (orange) shown.
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Doug Shepherd @dpshepherd.bsky.social · 06/03/2025
Out of nowhere, our institute just froze all indirect accounts - no matter when or where the indirects were generated. With completely unclear direction on how this works going forward. No words…
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Doug Shepherd @dpshepherd.bsky.social · 25/02/2025
In a brief respite from current events, I got to see a California Condor for the first time while running in the Grand Canyon this weekend! What an amazing animal. Unfortunately, public lands and those who protect them are also targets of this admin. Keeping fighting…
California condor perched on a rock with the Grand Canyon in the background.
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Doug Shepherd @dpshepherd.bsky.social · 04/02/2025
My partner told me today many community health centers (she works at one) may need to declare bankruptcy if the Federal funding freeze is allowed to continue. If you aren't familiar with CHCs, here is a good overview: www.kff.org/medicaid/iss...
kff.org
Community Health Center Patients, Financing, and Services | KFF
This brief reports on community health center patients, services, experiences, and financing in 2023 and analyzes changes from 2019 (pre-pandemic) through 2023 using data from the Uniform Data System ...
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Doug Shepherd @dpshepherd.bsky.social · 03/02/2025
A nice treat in this craziness. Ayush’s work on SIM reconstructions using physical noise modeling is out: www.nature.com/articles/s44... The low signal (avg of 16 photons/pixel) reconstructions, achieved without deep learning, are quite impressive in my opinion. We’re working on a faster GPU version
Left to right: pseudo-widefield, FISTA-SIM, Wiener filter SIM, and Bayesian SIM reconstructions of mitochondria labeled with PkMito Red in a live HeLa cell.

Top to bottom: decreasing signal, starting at an average of 762 photons per pixel and dropping to an average of 16 photons per pixel.
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Doug Shepherd @dpshepherd.bsky.social · 23/01/2025
We just got asked (aka told) to pause or cancel any HHS grant funded travel. Time to scramble to find flexible funds to send people places...
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Reposted by Doug Shepherd
Jennifer Waters @jencwaters.bsky.social · 07/01/2025
Join me, @talleylambert.bsky.social, @bethcimini.bsky.social, @florianjug.bsky.social & Hunter Elliott for our two week CSHL course on microscopy & image analysis starting March 24, 2025! Applications are due 1/31/25. meetings.cshl.edu/courses.aspx...
meetings.cshl.edu
Quantitative Imaging: From Acquisition to Analysis
Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.
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Doug Shepherd @dpshepherd.bsky.social · 06/01/2025
Anyone successfully dealt with chronic, at times crippling, facilities issues? It has really impacted the team's productivity, even though it's not their fault. I'm open to any and all advice beyond moving spaces. We already did that twice in 5 years with new (broken) promises each time.
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Doug Shepherd @dpshepherd.bsky.social · 19/12/2024
A bit of good fun at the gym helps to lighten up an insane week…
An indoor bouldering route with a Twilight movie picture and quote.
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Doug Shepherd @dpshepherd.bsky.social · 03/12/2024
Nick Galati (wp.wwu.edu/galatilab/) and I are recruiting a postdoc. The project is to study organelle distribution across protists with wildly different swimming strategies using bench work, expansion microscopy, and advanced light sheet microscopes. Full ad to come, please reach out if curious!
wp.wwu.edu
The Galati Lab |
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Doug Shepherd @dpshepherd.bsky.social · 30/11/2024
Nice morning run up Mt. Lowe in the San Gabriel mountains while visiting family. I love how many people, including families, get out and use these relatively steep trails in the Pasadena area. #running #trailrunning
View of the Cresenta valley and LA basin from the Middle Sam Merrill trail.
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Doug Shepherd @dpshepherd.bsky.social · 24/11/2024
It’s not all science all the time! Beautiful late Fall run in the Grand Canyon today. #trailrunning #running
Photo of Grand Canyon from South Khabib trailhead.Photo of the final switchbacks before the Colorado River in the Grand Canyon.Photo of the Colorado River in the Grand Canyon.
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Doug Shepherd @dpshepherd.bsky.social · 23/11/2024
We haven't imaged big samples in a few years. Recently Steven brought our custom ASLM, with some fun/interesting detection optics, back to life. Tatz Murakami graciously sent us a beautifully cleared and vasculature labeled mouse brain for imaging. Fused max projections of raw data.
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Doug Shepherd @dpshepherd.bsky.social · 18/11/2024
Today's adventure in academia. How many layers of IT do I need to contact to reset the fancy new Zoom TV system they put in our conference room. I'm betting greater than ten, but there are a still a few hours left in the day!
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Doug Shepherd @dpshepherd.bsky.social · 15/11/2024
Fluorescence Friday! 3D timelapse of MOLM-14 cells expressing GFP-LC3-RFP embedded in collagen. Orthoview rendering of GFP (cyan) and RFP (orange) imaged every 30 seconds using our Snouty-OPM.
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Doug Shepherd @dpshepherd.bsky.social · 11/11/2024
Slowly getting things settled in our (finally!) renovated labs. Part of the beam path in our multimodal setup for multicolor 2D-SIM and kilohertz 3D QPI.
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