Doug Shepherd @dpshepherd.bsky.social · 10/09/2026Glad it is useful and happy to help! Thanks for acknowledging here. 030
Doug Shepherd @dpshepherd.bsky.social · 10/12/2025Thanks! Your benchtop mesoSPIM paper was very helpful!! Confirmed a lot of what we were seeing and gave us the kick to finish this off. 110
Doug Shepherd @dpshepherd.bsky.social · 10/12/2025Additionally, @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 · 10/12/2025There are a lot of nice papers dealing with field curvature in LSFM, including work that from @nvladimus.bsky.social, @adamkglaser.bsky.social, @aakinwo.bsky.social, and others whose bluesky handles I don't know. 110
Doug Shepherd @dpshepherd.bsky.social · 10/12/2025We'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... 2123
Doug Shepherd @dpshepherd.bsky.social · 14/11/2025Special thanks to @moffittlab.bsky.social for a lot of help and advice along the way! More to come soon on speeding up the experimental side of large scale 3D spatial omics. 010
Doug Shepherd @dpshepherd.bsky.social · 14/11/2025If 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.orgGPU-accelerated, self-optimizing processing for 3D multiplexed iterative RNA-FISH experimentsImaging-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 ... 150
Doug Shepherd @dpshepherd.bsky.social · 06/11/2025We 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. 040
Doug Shepherd @dpshepherd.bsky.social · 28/10/2025We tried your FEP chamber setup and the results are great with an Olympus 60X/NA 1.0 water dipping and U-ExM ciliate samples. Thanks for putting it out there! 140
Reposted by Doug ShepherdAlexa 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 1128
Reposted by Doug ShepherdSmitha Maretvadakethope (she/her) @mathsmaret.bsky.social · 11/09/2025Our 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.orgPhilosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences: Vol 383, No 2304 085
Doug Shepherd @dpshepherd.bsky.social · 13/08/2025Accompanied 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/...science.orgUltrafast tomograms in a flashFourier 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... 000
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.orgFourier synthesis optical diffraction tomography for kilohertz rate volumetric imagingHighly multiplexed diffraction tomography enables kilohertz volume imaging for dynamic soft matter and biological systems. 151
Doug Shepherd @dpshepherd.bsky.social · 26/07/2025Tensorstore 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.comGitHub - 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 042
Doug Shepherd @dpshepherd.bsky.social · 26/07/2025We 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. 120
Doug Shepherd @dpshepherd.bsky.social · 23/06/2025We 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. 120
Doug Shepherd @dpshepherd.bsky.social · 17/06/2025Our 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. 130
Doug Shepherd @dpshepherd.bsky.social · 04/06/2025Spending 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... 0223
Doug Shepherd @dpshepherd.bsky.social · 09/04/2025Thanks! 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. 020
Doug Shepherd @dpshepherd.bsky.social · 09/04/2025As 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). 010
Doug Shepherd @dpshepherd.bsky.social · 09/04/2025Steven 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! 2202
Doug Shepherd @dpshepherd.bsky.social · 06/03/2025Out 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… 000
Doug Shepherd @dpshepherd.bsky.social · 25/02/2025In 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… 41047
Doug Shepherd @dpshepherd.bsky.social · 12/02/2025Super cool! Would be fun to play with at some point. 010
Doug Shepherd @dpshepherd.bsky.social · 04/02/2025This 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. 010
Doug Shepherd @dpshepherd.bsky.social · 04/02/2025CHCs 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. 100
Doug Shepherd @dpshepherd.bsky.social · 04/02/2025My 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.orgCommunity Health Center Patients, Financing, and Services | KFFThis 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 ... 111
Doug Shepherd @dpshepherd.bsky.social · 03/02/2025A 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 030
Doug Shepherd @dpshepherd.bsky.social · 29/01/2025Yeah, 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. 110
Doug Shepherd @dpshepherd.bsky.social · 29/01/2025Fixed the Cavendish experiment for our second semester advanced lab, fun with gravity! 310
Doug Shepherd @dpshepherd.bsky.social · 26/01/2025Finally 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? 010
Doug Shepherd @dpshepherd.bsky.social · 26/01/2025Having just rebuilt due to a lab move, I also vote for two galvo scanning for easier alignment. 110
Doug Shepherd @dpshepherd.bsky.social · 23/01/2025We 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... 010
Doug Shepherd @dpshepherd.bsky.social · 18/01/2025A 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. 020
Doug Shepherd @dpshepherd.bsky.social · 09/01/2025I got an e-bike a few years ago to help deal with the Arizona summers and added work/grocery panniers. >6k miles later, I only use a car for longer trips. One of the best investments I've ever made. 120
Reposted by Doug ShepherdJennifer Waters @jencwaters.bsky.social · 07/01/2025Join 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.eduQuantitative Imaging: From Acquisition to AnalysisCold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics. 15032
Doug Shepherd @dpshepherd.bsky.social · 06/01/2025Anyone 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. 000
Doug Shepherd @dpshepherd.bsky.social · 19/12/2024A bit of good fun at the gym helps to lighten up an insane week… 040
Doug Shepherd @dpshepherd.bsky.social · 03/12/2024This position will be part of the ASU Center for Biological Physics, ASU Center for Mechanisms of Evolution, and an NSF Biological Integration Institute - with plans to spend some time at Western Washington University working with the Galati lab on ciliates from the Salish Sea! 000
Doug Shepherd @dpshepherd.bsky.social · 03/12/2024Nick 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.eduThe Galati Lab | 100
Doug Shepherd @dpshepherd.bsky.social · 02/12/2024We are happy with the interleaved stabilization approach we currently use, if we build a new OPM we’ll definitely try it out. 000
Doug Shepherd @dpshepherd.bsky.social · 02/12/2024Yes, the drift is almost all temperature for us. We recently moved labs and things are much better now. We are doing some long experiments where we need to keep the instrument stable for week or more. 210
Doug Shepherd @dpshepherd.bsky.social · 02/12/2024Nice! We detect a shuttered 532 nm beam reflected off the back of the dichroic with the main camera, but have to stop fluorescence lasers and run the correction in between acquisition volumes. The continuous feedback in this approach is very elegant. 020
Doug Shepherd @dpshepherd.bsky.social · 30/11/2024Nice 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 040
Doug Shepherd @dpshepherd.bsky.social · 24/11/2024It’s not all science all the time! Beautiful late Fall run in the Grand Canyon today. #trailrunning #running 0330
Doug Shepherd @dpshepherd.bsky.social · 23/11/2024Paired with getting the instrument running again (he's writing that up now), Steven recently published some thoughts on modeling and optimizing remote focus pathways with large RI mismatches (opg.optica.org/oe/fulltext....)opg.optica.orgOptica Publishing Group 000
Doug Shepherd @dpshepherd.bsky.social · 23/11/2024We 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 · 18/11/2024Today'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! 020
