iiinova — where your digital self keeps evolving

Doug Shepherd @dpshepherd.bsky.social · 10/12/2025

Additionally, @adamezracohen.bsky.social group's paper that used this beast of an objective for widefield was very helpful when thinking about how to optimize the light path to retain as much performance as possible.

010

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.

2123

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.

040

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.

0223

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.

2202

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.

41047

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.

030

Doug Shepherd @dpshepherd.bsky.social · 29/01/2025

Fixed the Cavendish experiment for our second semester advanced lab, fun with gravity!

310

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.

040

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.

040

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.

0330

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.

262

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.

0101

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.

0211