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Reposted by Doug Shepherd

Smitha Maretvadakethope (she/her) @mathsmaret.bsky.social · 27d

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

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Doug Shepherd @dpshepherd.bsky.social · Aug 13

Accompanied by a nice perspective piece from our colleague Lei Tian, whose own work on high-information content computational imaging was a strong inspiration for our own.
www.science.org/doi/10.1126/...

Ultrafast tomograms in a flash

Fourier synthesis optical diffraction tomography encodes hundreds of views per exposure, enabling kilohertz-rate, label-free three-dimensional imaging of complex biological and soft-matter dynamics pr...

www.science.org

Doug Shepherd @dpshepherd.bsky.social · Aug 13

@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

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Doug Shepherd @dpshepherd.bsky.social · Jul 26

Tensorstore is much faster for read/write than vanilla zarr. Tools are here: github.com/QI2lab/opm-p...

Currently we only support our custom pymmcore-plus OPM format and ASI’s OPM format. Happy to work with you to support CZI LLSM files if you open an issue and provide some example data.

GitHub - QI2lab/opm-processing-v2: Code for fast deconvolution, deskewing, registration, and fusion of OPM/diSPIM/LLSM data.

Code for fast deconvolution, deskewing, registration, and fusion of OPM/diSPIM/LLSM data. - QI2lab/opm-processing-v2

github.com

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Doug Shepherd @dpshepherd.bsky.social · Jul 26

We have a bunch of fast skewed data handling tools (flatfield, decon, deskew, stitch) in Python, but they are not meant for real-time lazy viewing - we do that in our own custom acq. software. We use Tensorstore to write with compression at reasonably fast speeds.

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Doug Shepherd @dpshepherd.bsky.social · Jun 23

We use a number of FLIR and Basler cameras with the high end Sony CMOS chips. For short exposures, they can work well. Another thing to look out for is that the hot pixels fluctuate on top of the true dead pixels. We correct a static map and then do a second correction that looks for outliers.

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Doug Shepherd @dpshepherd.bsky.social · Jun 17

Our experience is the dark current (no cooling) and dead pixels (quality control) are higher than your standard sCMOS. We've mapped the pixel by pixel gain for a few different industrial CMOS chips and often find some non-linearities.

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Doug Shepherd @dpshepherd.bsky.social · Jun 4

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 · Apr 9

Thanks! We use a Nikon 100x/1.35 silicone oil for O1. The objectives in the setup are still the same as our previous Snouty-OPM papers.

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Doug Shepherd @dpshepherd.bsky.social · Apr 9

As usual, all the code is developed in the open at our github. Control: github.com/QI2lab/opm-v2 and processing: github.com/QI2lab/opm-p....

The control code is fully hardware triggered and pretty performant already. We are actively working on speeding parts of the processing (fusion to ome-zarr).

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Doug Shepherd @dpshepherd.bsky.social · Apr 9

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 · Mar 6

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…

Doug Shepherd @dpshepherd.bsky.social · Feb 25

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 · Feb 21

Thank you!

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Doug Shepherd @dpshepherd.bsky.social · Feb 12

Super cool! Would be fun to play with at some point.

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Doug Shepherd @dpshepherd.bsky.social · Feb 4

This is yet another reason (in addition to MANY others) to call your representatives and senators. Likely more is going to be required, but it's a starting point.

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Doug Shepherd @dpshepherd.bsky.social · Feb 4

CHCs served roughly 31 million people in 2023, 90% of which were at or below 200% the federal poverty level. That includes roughly 9.1 million pediatric patients.

Despite the court orders and the executive branch's claim that Medicaid is not effected, their Medicaid funding portals remain frozen.

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Doug Shepherd @dpshepherd.bsky.social · Feb 4

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

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Doug Shepherd @dpshepherd.bsky.social · Feb 3

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 · Jan 29

Yeah, lead spheres and torsion bar suspended by 20 micron diameter tungsten wire. It's a really nice setup, but tricky for them to get right because of how long it takes to settle down before you can take data.

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Doug Shepherd @dpshepherd.bsky.social · Jan 29

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

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Doug Shepherd @dpshepherd.bsky.social · Jan 26

Finally got the promised lab space >5 years after I uprooted the lab from Colorado…so a bit of column A and a bit of column B?

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Doug Shepherd @dpshepherd.bsky.social · Jan 26

Having just rebuilt due to a lab move, I also vote for two galvo scanning for easier alignment.

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Doug Shepherd @dpshepherd.bsky.social · Jan 23

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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Doug Shepherd @dpshepherd.bsky.social · Jan 18

A number of us as graduate students were involved in one in condensed matter physics. Nearly all of us (across many institutions) bailed from that field, but managed to stay in science somehow. I don’t think it moved science forward and just created a lot of hard feelings.

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