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Josh Dickerson

@joshdcryoem.bsky.social
218 followers 244 following 9 posts

PostDoc in Lucas Lab at UC Berkeley. Formerly PhD student in Russo group at MRC-LMB and Master's student in Garman group at Univ. Oxford.

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Reposted by Josh Dickerson
Bronwyn Lucas @bronwynalucas.bsky.social · 12/08/2026
Now on Arxiv: arxiv.org/abs/2608.10029 Led by grad student Matthew Giammar and collaborator Alex Strang, we provide a fast algorithm to calculate a low rank approximation to large (>100 million row) matrices with high fidelity that will accelerate template matching.
arxiv.org
A fast diagonalization algorithm to enable singular value decomposition of large matrices for efficient template matching
Many computational problems possess the following three features: (1) the problem could be solved efficiently if a linear operator could be diagonalized, (2) direct diagonalization is infeasible due t...
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Reposted by Josh Dickerson
SBGrid Consortium @sbgrid.bsky.social · 05/08/2026
New Title Alert: Leopard-EM (Location & oriEntatiOn of PARticles found using two-Dimensional tEmplate Matching) is a python package for running two-dimensional template matching (2DTM) on cryo-EM images. More here: buff.ly/FZ5bVfZ #SBGrid #Software #StructuralBiology
lucaslab-berkeley.github.io
Leopard-EM Homepage - Leopard-EM: Two-Dimensional Template Matching in Python
Overview of the Leopard-EM package for 2DTM in Python
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Reposted by Josh Dickerson
Laina Hall @lainahall.bsky.social · 25/07/2026
With Cryo-ET/EM, the macromolecules we study (and biological questions we ask) are SNR-limited. Here, we share Nilas, a low-voltage milling method named after thin sea ice. Nilas produces thin (sub 50 nm in places!), minimally damaged lamellae. biorxiv.org/content/10.64898/2026.07.21.739890v1
biorxiv.org
Optimized cryo-FIB milling strategy to generate thin, minimally damaged biological lamellae
Focused ion beam (FIB)-milling has been adapted to thin frozen cells for visualization of macromolecular structures in situ with cryogenic electron microscopy. However, only a few large and abundant c...
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Josh Dickerson @joshdcryoem.bsky.social · 06/06/2026
XLPP in practice www.biorxiv.org/content/10.6...
biorxiv.org
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Reposted by Josh Dickerson
bioRxivpreprint @biorxivpreprint.bsky.social · 14/05/2026
High Accuracy Fluorescence Guided Focused Ion Beam Milling www.biorxiv.org/content/10.64898/20…
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Reposted by Josh Dickerson
Marten Chaillet @martenchaillet.bsky.social · 03/05/2026
MissAlignment is out!!! Our new software that improves reference-free tilt series alignment by mimicking human intuition. Check out Dimitry's beautiful thread for a quick summary! And the preprint for more details: www.biorxiv.org/content/10.6... The program: github.com/warpem/miss-...
biorxiv.org
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Reposted by Josh Dickerson
IMPRS for Living Matter @imprs-lm.bsky.social · 17/03/2026
📣 Physicists and engineers: apply your experimental skills to biology! Join the group of Katerina Naydenova @imprs-lm.bsky.social for a #PhD to develop new technologies that enable answering fundamental biological questions. Apply NOW!
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Josh Dickerson @joshdcryoem.bsky.social · 08/12/2025
Now out in full form. Again, a big thanks to #teamtomo and @alisterburt.bsky.social for developing the infrastructure to build this on. journals.iucr.org/d/issues/202...
journals.iucr.org
Leopard-EM: an extensible 2D template-matching package to accelerate in situ structural biology
In situ cryo-EM coupled with 2D template matching (2DTM) holds the potential to visualize the cellular structureome in context, but further developments are required to make this a reality. We describ...
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Reposted by Josh Dickerson
MRC Laboratory of Molecular Biology @mrclmb.ac.uk · 22/10/2025
Chris Russo and Anastasiia Gusach have developed a new method to prepare #cryoEM samples that avoids protein damage during freezing Read more: www2.mrc-lmb.cam.ac.uk/a-new-method... #LMBResearch
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Reposted by Josh Dickerson
MPI Dortmund @mpi-dortmund.bsky.social · 07/10/2025
We are happy to announce that we will have two new scientific groups led by Andrija Sente and Katerina Naydenova soon! If you are interested to join their lab as a PhD Student apply at our @imprs-lm.bsky.social www.imprs-lm.mpg.de/index.php/jo...
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Reposted by Josh Dickerson
cryoEM papers @cryoempapers.bsky.social · 17/09/2025
Improved cryo-EM reconstruction of sub-50 kDa complexes using 2D template matching www.biorxiv.org/content/10.1101/2025.09.11.675606v1 #cryoEM
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Josh Dickerson @joshdcryoem.bsky.social · 30/08/2025
Happy for this to be out! We have documentation and tutorials here. Please give it a try and let us know what you think. lucaslab-berkeley.github.io/Leopard-EM/
lucaslab-berkeley.github.io
Leopard-EM Homepage - Leopard-EM: Two-Dimensional Template Matching in Python
Overview of the Leopard-EM package for 2DTM in Python
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Reposted by Josh Dickerson
cryoEM papers @cryoempapers.bsky.social · 02/08/2025
Pulsed-electron illumination does not reduce beam damage for imaging biological macromolecules www.biorxiv.org/content/10.1101/2025.07.29.667395v1 #cryoEM
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Reposted by Josh Dickerson
Bronwyn Lucas @bronwynalucas.bsky.social · 25/07/2025
@joshdcryoem.bsky.social will also be giving a talk about his prior work as a PhD student with Chris Russo developing strategies to take advantage of the reduced radiation damage at liquid Helium temperatures for cryo-EM. You can find their paper here: www.pnas.org/doi/abs/10.1...
pnas.org
Reducing the effects of radiation damage in cryo-EM using liquid helium temperatures | PNAS
The physical limit in determining the atomic structure of biological molecules is radiation damage. In electron cryomicroscopy, there have been num...
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Reposted by Josh Dickerson
Bronwyn Lucas @bronwynalucas.bsky.social · 25/07/2025
If you are going to M&M, also see postdoc @joshdcryoem.bsky.social's poster about tilted vs untilted data collection for in situ structural biology www.sciencedirect.com/science/arti....
sciencedirect.com
To tilt or not to tilt? Strategies for in situ cryo-EM data collection
Recent breakthroughs in single-particle cryogenic electron microscopy (cryo-EM) and protein structure prediction have transformed our ability to resol…
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Josh Dickerson @joshdcryoem.bsky.social · 28/06/2025
Check out our recent review discussing the merits of tilt series vs single micrographs for in situ cryo-EM! www.sciencedirect.com/science/arti...
sciencedirect.com
To tilt or not to tilt? Strategies for in situ cryo-EM data collection
Recent breakthroughs in single-particle cryogenic electron microscopy (cryo-EM) and protein structure prediction have transformed our ability to resol…
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Reposted by Josh Dickerson
Lewys Jones @lewysj.bsky.social · 20/05/2025
At the 2024 IMC meeting, Richard Henderson laid down a challenge. Design a #TEM single-particle #cryoEM lens with 1mm Cc at 100kV. I'm thrilled to reveal our new Arxiv preprint delivering a fully retrofittable pole-piece swap out for the @jeoleurope.bsky.social 1400 TEM. arxiv.org/abs/2505.11458
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Reposted by Josh Dickerson
Alister Burt @alisterburt.bsky.social · 12/05/2025
In the Bay Area? Love computational cryo-EM/ET? Come join us for the first edition of FrostByte - a meeting for the local computational cryo-EM methods community! Details and registration at frostbyte-cryoem.github.io Thanks to @joshdcryoem.bsky.social and Ariana Peck for help organizing!
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Josh Dickerson @joshdcryoem.bsky.social · 23/04/2025
For a shorter read, @mrclmb.bsky.social and @science.org also have articles about the helium story. www.science.org/content/arti...
science.org
Ultracool microscopy yields a sharper look at proteins
After years of frustration, researchers learn how to sharpen molecular images with liquid helium
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Josh Dickerson @joshdcryoem.bsky.social · 23/04/2025
After years parked at a Polara, I’m excited to share that my PhD work is finally out! We figured out why imaging at liquid helium temperatures wasn’t working—and how to fix it. 🔗 www.pnas.org/doi/10.1073/...
pnas.org
Reducing the effects of radiation damage in cryo-EM using liquid helium temperatures | PNAS
The physical limit in determining the atomic structure of biological molecules is radiation damage. In electron cryomicroscopy, there have been num...
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Reposted by Josh Dickerson
bioRxiv Biophysics @biorxiv-biophys.bsky.social · 06/04/2025
Exploring shaped focused ion beams for lamella preparation www.biorxiv.org/content/10.1101/202…
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Reposted by Josh Dickerson
bioRxiv Biophysics @biorxiv-biophys.bsky.social · 31/03/2025
In-Situ High-Resolution Cryo-EM Reconstructions from CEMOVIS www.biorxiv.org/content/10.1101/202…
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Reposted by Josh Dickerson
bioRxiv Biophysics @biorxiv-biophys.bsky.social · 12/03/2025
Foam film vitrification for cryo-EM www.biorxiv.org/content/10.1101/202…
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Josh Dickerson @joshdcryoem.bsky.social · 18/01/2025
I've been wanting to see a paper using off-axis electron holography for low-dose biological imaging since the start of my PhD. Spatially resolved charge measurements👌
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Reposted by Josh Dickerson
IUCrJ @iucrj.iucr.org · 18/01/2025
Kexin Zhang et al.: A new statistical metric for robust target detection in cryo-EM using 2D template matching #3DReconstructionAndImageProcessing #SingleParticleCryoEM #Imaging @umassboston...#IUCr journals.iucr.org/paper?S2052252524…
journals.iucr.org
A new statistical metric for robust target detection in cryo-EM using 2D template matching
A novel statistical metric for 2D template matching (2DTM), the 2DTM p-value, has been developed to improve the detection of targets in cryo-EM images under various imaging and sample conditions, particularly for smaller and aspherical targets.
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Reposted by Josh Dickerson
cryoEM papers @cryoempapers.bsky.social · 22/11/2024
Laser Flash Melting Cryo-EM Samples to Overcome Preferred Orientation biorxiv.org/cgi/content/short/2024.11.21.624652v1
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