Doug Shepherd
recovering alpinist and scientist.
- 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...
- There 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.
- 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...
- 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.
- Reposted by Doug Shepherd[Not loaded yet]
- Reposted by Doug Shepherd[Not loaded yet]
- @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...
- 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…
- 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…
- 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
- 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 ShepherdJoin 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...
