hardware x software in microscopy | views are graphical projections | postdoc in Ries Lab @MaxPerutzLabs | @zacsimile.bsky.social | 🇺🇸 in 🇦🇹 | he/him
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Joined January 2017
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Zach Marin retweeted
Long time in the making and finally out. Great work by @haydnspass and @hitshah95 who wrote the code, Maxime and Nestor for the beautiful samples and
@zacsimile for helping to wrap this up. Try it out!
[0/1] Excited to share our new preprint DECODE-Plex! After many people efforts, we developed a deep-learning framework for multi-channel SMLM, enabling simultaneous localization and color assignment of densely packed emitters across multiple channels.
biorxiv.org/content/10.64898…
MINFLUX works well in theory, but system and sample imperfections can lead to suboptimal resolution. To address this, @JonasRies and I developed SimuFLUX: biorxiv.org/content/10.1101/…, a realistic simulator to optimize MINFLUX experiments before samples go on the microscope.
For single molecule tracking, we optimized laser power, pattern size, photon limit and pattern dwell time to increase the measurable diffusion coefficient by 70% over that captured by the standard Abberior tracking sequence.
These and many other simulations are covered in the paper. Example notebooks for each simulation are provided in the code base, and on Google Colab (see github.com/ries-lab/SimuFLUX…). We hope the community will find this useful and contribute their own examples using this package.
Starting off simple: misalignment of the phase pattern that generates a donut degrades performance, while misalignment of the pinhole has little effect.
Zach Marin retweeted
Our manuscript on accelerating OPM / SCAPE acquisition rate via aliasing is online now:
opg.optica.org/boe/fulltext.…
Our work addresses the issue that an OPM PSF is tilted, and as such it leaves a lot of "empty space" in Fourier space (FFT of experimental data on the right)... 1/n
Zach Marin retweeted
4Pi-SMS and pan-ExM reveal, in a close collaboration with the Rothman lab, a surprising tetraplex organization and self-assembly of rim golgins, which we believe can explain stack formation of the Golgi apparatus:
biorxiv.org/content/10.1101/…
Zach Marin retweeted
I am happy to share our 5-year's work of manual mapping of all the native proteins in the golgin family, providing the highest resolution atlas of the Golgi apparatus to date! Yes, we can distinguish proteins at different cisternae.
Zach Marin retweeted
I’m excited to share our latest research from @musser_lab , published today in @Nature. Using two-color 3D MINFLUX, we directly visualized nuclear import and export events through transport-active nuclear pores.
nature.com/articles/s41586-0…
Zach Marin retweeted
🎉Just out in @NaturePhotonics : rdcu.be/ecthU
Our Review describing the revolutionary principle behind #MINFLUX🔬, summarizing major imaging and tracking breakthroughs and giving an outlook on future advancements.
Big thanks to @JonasRies & @zacsimile. @MaxPerutzLabs
Zach Marin retweeted
Our manuscript for remote focus stabilization for oblique plane microcopy is online:
opg.optica.org/boe/fulltext.…
Zach Marin retweeted
Excited to share LUNAR (Localization Using Neural-physics Adaptive Reconstruction) —a self-supervised, blind localization method that combines neural networks & physics to estimate aberrations from overlapped blinking molecules for large DOF imaging. Great work @judefffff !
Neural-physics adaptive reconstruction reveals 3D subcellular nanostructures over a large depth of field biorxiv.org/content/10.1101/… #biorxiv_biophys