Microscopy preprints – new tools and techniques in imaging

Posted by FocalPlane, on 12 January 2024

Here is a curated selection of preprints posted recently on new tools and techniques in imaging. Let us know if we are missing any recent preprints that are on your reading list!

The Benchtop mesoSPIM: a next-generation open-source light-sheet microscope for large cleared samples
Nikita Vladimirov, Fabian F. Voigt, Thomas Naert, Gabriela R. Araujo, Ruiyao Cai, Anna Maria Reuss, Shan Zhao, Patricia Schmid, Sven Hildebrand, Martina Schaettin, Dominik Groos, José María Mateos, Philipp Bethge, Taiyo Yamamoto, Valentino Aerne, Alard Roebroeck, Ali Ertürk, Adriano Aguzzi, Urs Ziegler, Esther Stoeckli, Laura Baudis, Soeren S. Lienkamp, Fritjof Helmchen

A super-resolution compatible workflow for highly multiplexed immunofluorescence of routinely processed kidney tissue
Florian Siegerist, Svenja Kitzel, Nihal Telli, Juan Saydou Dikou, Vedran Drenić, Christos E. Chadjichristos, Christos Chatziantoniou, Nicole Endlich

Mantis: high-throughput 4D imaging and analysis of the molecular and physical architecture of cells
Ivan E. Ivanov, Eduardo Hirata-Miyasaki, Talon Chandler, Rasmi Cheloor Kovilakam, Ziwen Liu, Chad Liu, Manuel D. Leonetti, Bo Huang, Shalin B. Mehta

Optical constraints on two-photon voltage imaging
Hunter C. Davis, F. Phil Brooks III, J. David Wong-Campos, Adam E. Cohen

Figure extracted from Davis, *et al.* made available under a CC-BY-NC 4.0 International license.

Phase diversity-based wavefront sensing for fluorescence microscopy
Courtney Johnson, Min Guo, Magdalena C. Schneider, Yijun Su, Satya Khuon, Nikolaj Reiser, Yicong Wu, Patrick La Riviere, Hari Shroff

Towards ultra-low-cost smartphone microscopy
Haoran Zhang, Weiyi Zhang, Zirui Zuo, Jianlong Yang

A Structured Illumination Microscopy Framework with Spatial-Domain Noise Propagation
Ayush Saurabh, Peter T. Brown, J. Shepard Bryan IV, Zachary R. Fox, Rory Kruithoff, Douglas P. Shepherd, Steve Pressé

Open-top Bessel beam two-photon light sheet microscopy for three-dimensional pathology
Won Yeong Park, Jieun Yun, Jinho Shin, Byung Ho Oh, Gilsuk Yoon, Seung-Mo Hong, Ki Hean Kim

Figure extracted from Park, *et al.* made available under a CC-BY 4.0 International license..

High-speed Auto-Polarization Synchronization Modulation Three-dimensional Structured Illumination Microscopy
Yaning Li, Ruijie Cao, Wei Ren, Yunzhe Fu, Yiwei Hou, Suyi Zhong, Karl Zhanghao, Meiqi Li, Peng Xi

Enhancing Light-Sheet Fluorescence Microscopy Illumination Beams through Deep Design Optimization
Chen Li, Mani Ratnam Rai, Yuheng Cai, H. Troy Ghashghaei, Alon Greenbaum

Building a super-resolution fluorescence cryomicroscope
Mart G. F. Last, Lenard M. Voortman, Thomas. H. Sharp

Aberration correction for deformable mirror based remote focusing enables high-accuracy whole-cell super-resolution imaging
Wei Shi, Yingchuan He, Jianlin Wang, Lulu Zhou, Jianwei Chen, Liwei Zhou, Zeyu Xi, Zhen Wang, Ke Fang, Yiming Li

Figure extracted from Shi, *et al.* made available under a CC-BY 4.0 International license.

Label-free 3-D molecular imaging of living tissues using Raman Spectral Projection Tomography
Elzbieta Stepula, Anders R. Walther, Dev Mehrotra, Magnus Jensen, Mu H. Yuan, Simon V. Pedersen, Eileen Gentleman, Michael B. Albro, Martin A. B. Hedegaard, Mads S. Bergholt

Increased multiplexity in optical tissue clearing-based 3D immunofluorescence microscopy of the tumor microenvironment by LED photobleaching
Jingtian Zheng, Yi-Chien Wu, Evan H. Phillips, Xu Wang, Steve Seung-Young Lee

Rapid in-EPON CLEM for everyone: Combining fast and efficient labeling of self-labeling enzyme tags with EM-resistant Janelia Fluor dyes
Rico Franzkoch, Sabrina Wilkening, Viktoria Liss, Michael Holtmannspötter, Rainer Kurre, Olympia E. Psathaki, Michael Hensel

Figure extracted from Franzkoch, *et al.* made available under a CC-BY 4.0 International license.

Fast imaging of millimeter-scale areas with beam deflection transmission electron microscopy
Zhihao Zheng, Christopher S. Own, Adrian A. Wanner, Randal A. Koene, Eric W. Hammerschmith, William M. Silversmith, Nico Kemnitz, Ran Lu, David W. Tank, H. Sebastian Seung

Deep MALDI-MS Spatial ‘Omics guided by Quantum Cascade Laser Mid-infrared Imaging Microscopy
Lars Gruber, Stefan Schmidt, Thomas Enzlein, Huong Giang Vo, James Lucas Cairns, Yasemin Ucal, Florian Keller, Denis Abu Sammour, Rüdiger Rudolf, Matthias Eckhardt, Stefania Alexandra Iakab, Laura Bindila, Carsten Hopf

Lanthanide Cathodophores for Multicolor Electron Microscopy
Sohaib Abdul Rehman, Jeremy B. Conway, Amy Nichols, Edward R. Soucy, Amanda Dee, Kristal Stevens, Simon Merminod, Isabella MacNaughton, Abigail Curtis, Maxim B. Prigozhin

Detection of Fluorescent Protein Mechanical Switching in Cellulo
Timothy Curtis Shoyer Jr., Kasie L Collins, Trevor R Ham, Aaron T Blanchard, Juilee N Malavade, Jennifer L West, Brenton D Hoffman

Oblique Line Scan Illumination Enables Expansive, Accurate and Sensitive Single Protein Measurements in Solution and in Living Cells
Amine Driouchi, Mason Bretan, Brynmor J. Davis, Alec Heckert, Markus Seeger, Maité Bradley Silva, William SR. Forrest, Jessica Hsiung, Jiongyi Tan, Hongli Yang, David T. McSwiggen, Linda Song, Askhay Sule, Behnam Abaie, Brianna Conroy, Liam A. Elliott, Eric Gonzalez, Fedor Ilkov, Joshua Isaacs, George Labaria, Michelle Lagana, Delaine D. Larsen, Brian Margolin, Mai K. Nguyen, Jeremy Rine, Yangzhong Tang, Martin Vana, Andrew Wilkey, Zhengjian Zhang, Stephen Basham, Jaclyn J. Ho, Stephanie Johnson, Aaron A. Klammer, Kevin Lin, Xavier Darzacq, Eric Betzig,

A Fast Interferometric Beam Shaper for Multi-Emitter 3D MINFLUX
Maximilian K. Geismann, Alba Gomez-Segalas, Alessandro Passera, Mehrta Shirzadian, Francisco Balzarotti

Figure extracted from Geismann, *et al.* made available under a CC-BY 4.0 International license.

The Rise of Data-Driven Microscopy powered by Machine Learning
Leonor Morgado, Estibaliz Gómez-de-Mariscal, Hannah S. Heil, Ricardo Henriques

Figure extracted from Morgado, *et al.* made available under a CC-BY 4.0 International license.

User-friendly Oblique Plane Microscopy on a fully functional commercially available microscope base
George Sirinakis, Edward S. Allgeyer, Dmitry Nashchekin, Daniel St Johnston

Figure extracted from Sirinakis, *et al.* made available under a CC-BY 4.0 International license.

Imaging neuronal voltage beyond the scattering limit
Tsai-Wen Chen, Xian-Bin Huang, Sarah E. Plutkis, Katie L. Holland, Luke D. Lavis, Bei-Jung Lin

The two key substitutions in the chromophore environment of mKate2 to produce an enhanced FusionRed-like red fluorescent protein
Dmitry A. Ruchkin, Alexey S. Gavrikov, Danila V. Kolesov, Andrey Yu. Gorokhovatsky, Tatiana V. Chepurnykh, Alexander S. Mishin, Eugene G. Maksimov, Nadya V. Pletneva, Vladimir Z. Pletnev, Konstantin A. Lukyanov, Alexey M. Bogdanov

HiExM: high-throughput expansion microscopy enables scalable super-resolution imaging
John H Day, Pema Maretich, Catherine M Della Santina, Alex L Auld, Kirsten K Schneider, Tay Shin, Edward S Boyden, Laurie A Boyer

IsoVEM: Isotropic Reconstruction for Volume Electron Microscopy Based on Transformer
Jia He, Yan Zhang, Wenhao Sun, Ge Yang, Fei Sun

Surpassing Challenges in Structured-Illumination Microscopy with FlexSIM
Emmanuel Soubies, Alejandro Nogueron, Florence Pelletier, Thomas Mangeat, Christophe Leterrier, Michael Unser, Daniel Sage

Event-based Single Molecule Localization Microscopy (eventSMLM) for High Spatio-Temporal Super-resolution Imaging
Jigmi Basumatary, S Aravinth, Neeraj Pant, Vignesh Ramanathan, Chetan Singh Thakur, Partha Pratim Mondal

Single-molecule detection and super-resolution imaging with a portable and adaptable 3D-printed microscopy platform (Brick-MIC)
Gabriel G. Moya Muñoz, Oliver Brix, Philipp Klocke, Nicolas D. Wendler, Eitan Lerner, Niels Zijstra, Thorben Cordes

Deep super-resolution imaging of thick tissue using structured illumination with adaptive optics
Jingyu Wang, Danail Stoychev, Mick Phillips, David Miguel Susano Pinto, Richard M. Parton, Nick Hall, Josh Titlow, Ana Rita Faria, Matthew Wincott, Dalia Gala, Andreas Gerondopoulos, Niloufer Irani, Ian Dobbie, Lothar Schermelleh, Martin Booth, Ilan Davis

Correlative single-cell hard X-ray tomography and X-ray fluorescence imaging
Zihan Lin, Xiao Zhang, Purbasha Nandi, Yuewei Lin, Liguo Wang, Yong Chu, Timothy Paape, Yang Yang, Xianghui Xiao, Qun Liu