Doug Shepherd
@dpshepherd.bsky.social
recovering alpinist and scientist.
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...
www.biorxiv.org/content/10.1...
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 ...
www.biorxiv.org
November 14, 2025 at 2:13 AM
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...
www.biorxiv.org/content/10.1...
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.
Max projection xy&xz views of expanded paramecium and tetrahymena cells. Scale bar is ~5.5 um accounting for expansion. Epifluorescence + deconvolution.
November 6, 2025 at 9:41 PM
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.
Max projection xy&xz views of expanded paramecium and tetrahymena cells. Scale bar is ~5.5 um accounting for expansion. Epifluorescence + deconvolution.
Reposted by Doug Shepherd
🔬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
Questions? Ask here or DM me.
@mblscience.bsky.social @aqlm.bsky.social
#microscopy #fluorescence
October 27, 2025 at 5:37 PM
🔬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
Questions? Ask here or DM me.
@mblscience.bsky.social @aqlm.bsky.social
#microscopy #fluorescence
Reposted by Doug Shepherd
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...
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences: Vol 383, No 2304
royalsocietypublishing.org
September 11, 2025 at 8:59 AM
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...
@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/...
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.
www.science.org
August 13, 2025 at 6:17 PM
@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/...
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...
June 4, 2025 at 6:56 PM
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...
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!
April 9, 2025 at 3:43 AM
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!
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…
No words…
March 6, 2025 at 9:22 PM
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…
No words…
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…
Unfortunately, public lands and those who protect them are also targets of this admin. Keeping fighting…
February 25, 2025 at 12:35 AM
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…
Unfortunately, public lands and those who protect them are also targets of this admin. Keeping fighting…
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...
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 ...
www.kff.org
February 4, 2025 at 12:20 AM
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...
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
February 3, 2025 at 9:57 PM
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
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...
January 23, 2025 at 11:12 PM
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...
Reposted by Doug Shepherd
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...
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.
meetings.cshl.edu
January 7, 2025 at 6:42 PM
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...
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.
January 6, 2025 at 10:31 PM
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.
A bit of good fun at the gym helps to lighten up an insane week…
December 19, 2024 at 1:58 AM
A bit of good fun at the gym helps to lighten up an insane week…
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!
The Galati Lab |
wp.wwu.edu
December 3, 2024 at 9:50 PM
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!
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
November 30, 2024 at 6:06 PM
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
It’s not all science all the time! Beautiful late Fall run in the Grand Canyon today. #trailrunning #running
November 24, 2024 at 9:34 PM
It’s not all science all the time! Beautiful late Fall run in the Grand Canyon today. #trailrunning #running
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.
November 23, 2024 at 6:23 PM
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.
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!
November 18, 2024 at 10:01 PM
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!
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.
November 15, 2024 at 10:39 PM
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.
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.
November 11, 2024 at 12:36 AM
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.