Doug Shepherd
@dpshepherd.bsky.social
recovering alpinist and scientist.
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.
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!
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…
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
Fixed the Cavendish experiment for our second semester advanced lab, fun with gravity!
January 29, 2025 at 1:52 AM
Fixed the Cavendish experiment for our second semester advanced lab, fun with gravity!
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…
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.
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.