Microscopy preprints – new tools and techniques in imaging

Posted by FocalPlane, on 30 October 2026

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

Sample preparation optimisation for array tomography volume EM of entire organisms: a case study for marine larvae
Kata Szabó, Alexandra Kerbl, Karel Mocaer, Angelika Svetlove, Alexandra Pacureanu, Gáspár Jékely

Figure extracted from Szabó, *et al.* The image is made available under a CC-BY 4.0 International license.

Whole cryo-FIB lamella acquisition at high magnification with rectangular beam montage cryo-electron tomography
Hamish G. Brown, Sepideh Valimehr, Denver Styczynski, Manasi Mudaliyar, Srujan Shetty Kundapura, Matthew D. Johnson, Debnath Ghosal, Eric Hanssen

Nanophotonic DyeCycling delivers single-molecule FRET beyond photobleaching to identify heterogenous dynamics in DNA and protein systems
Benjamin Vermeer, Dong Hoon Shin, Alexander Vogel, Fabian Zundel, Sabina Caneva, Sonja Schmid

Intronised fluorophores improve reporter output and biosensor expression in plants
Sebastian Samwald, Tom Schreiber, Tonni Grube Andersen

Fast single molecule localization microscopy in 3D
Edward S. Allgeyer, Jennifer H. Richens, Jeanne Lefévère-Laoide, Ewa K. Paluch, George Sirinakis, Daniel St Johnston

Figure extracted from Allgeyer, *et al.* The image is made available under a CC-BY 4.0 International license.

Hybrid Transport-of-Intensity and Polarization Differential Phase Contrast for Extended Spatial-Frequency Phase Imaging
Fraser Montandon, Jasmin Knopp, Caron A. Jacobs, Fred Nicolls

Ratio-preserving super-resolution FLIM for quantitative live-cell lifetime imaging
Chenyang Li, Linglong Li, Yiwen Cheng, Wenqing Lu, Wen Gou, Haoyu Li, Qi Zou, Dilizhatai Saimi, Zhixing Chen, Wenjia Gu, Youjun Wang, Changliang Guo, Bei Liu, Xiaoshuai Huang, Junchao Fan, Liangyi Chen

Bayesian in situ point spread function modeling enables high-fidelity three-dimensional nanoscopy in deep tissue
Jian Cao, Yumian Li, Yuyuan Qiao, Tailong Chen, Yiqing Zhang, Hao-Cheng Gao, Junyi Zhang, Lirong Qiu, Jianli Liu, Fan Xu

Workflow and instrumentation for multiscale correlative imaging in voluminous cryogenic specimens
Edoardo D’Imprima, Evgenia Zagoriy, Saskia Mimietz-Oeckler, Robert Kirmse, Andreas Hallady, Philip Nkemdirim Mbonu, Paolo Ronchi, Martin Jechlinger, Julia Mahamid

Figure extracted from D’Imprima, *et al.* The image is made available under a CC-BY 4.0 International license.

A simple platform for in situ DNA-PAINT optimization enables improved multiplexed super-resolution imaging in Gram-negative bacteria
Kilian Andress, Paul Said Köhler, Ruilan Xu, Alica Schmidt-Heydt, Andreas Diepold, Christoph Spahn

Figure extracted from Andress, *et al.* The image is made available under a CC-BY 4.0 International license.

Multi-region two-photon calcium imaging in freely moving animals
Embla Kjellevold-Skallerud, Shouwen Ma, Julija Arbaciauskaite, Rajat Saxena, Antonio Lorca Camara, Klaus Joran Jenssen, Jonathan Robert Whitlock, Gahr Manfred, Weijian Zong

Adaptation of Iterative Ultrastructure Expansion Microscopy (iU-ExM) enables high-resolution imaging of the cytoskeleton and subcellular architecture of Trypanosoma cruzi
Normanda Souza-Melo, Giovanna Henriques de Souza, Sharmila Ortiz, Wanderley De Souza

Figure extracted from Souza-Melo, *et al.* The image is made available under a CC-BY 4.0 International license.

Quanta microscopy enables fluorescence imaging at the native bit-plane rate
Jooyeong Yun, Keyi Han, Aleksandra Janusz-Kaminska, Wenhao Zhang, Zhi Ling, Yan Huang, Chunhui Xu, Gary J. Bassell, Shu Jia

Adaptive-optics lattice light-sheet microscopy enables correlative single-molecule imaging of endogenous proteins in native environments
Maxime Malivert, Chiara C. Galizia, Bram A.A.J.W. Willems, Magali Mondin, Cécile Lemoigne, Paul Lecompte Saint-Jean, Barthélémy Demeer, Maximilien Marcelino, Dario Crippa, Olivier Thoumine, Fabrice Harms, Matthieu Sainlos, Daniel Choquet, Mathieu Ducros, Angela M. Getz

An open-source, 3D-printable droplet microfluidics platform with strobe-enhanced microscopy
Pierre Padilla-Huamantinco, Matias Hurtado-Labarca, Christie Nel, Tomas Astudillo, Wladimir Araya, Juan José Leon, Josefina Belen Reyes Arroyo, Tobias Wenzel

Rapid femtosecond laser trenching accelerates cryo-electron tomography lamella workflows
Christian M. Orr, Pranav N. M. Shah, Éilís C. Bragginton, Saikat Chakraborty, Helen M. E. Duyvesteyn, Stephen Riggs, David I. Stuart, Armin Wagner

Replacing H2O with D2O in cryo-EM reduces radiation damage in biological samples
Min Chevalier Kwon, Senik Matinyan, Eric van Genderen, Jan Pieter Abrahams

Fluorescent Biosensors for Cryogenic Correlative Light and Electron Microscopy
Christopher A. Azaldegui, Kevin M. Rose, Davis Perez, Jacob A. Summers, Claudia A. Mak, William P. Dwyer, Anthony G. Vecchiarelli, Julie S. Biteen, José R. Dinneny, Peter D. Dahlberg

Figure extracted from Azaldegui, *et al.* The image is made available under a CC-BY 4.0 International license.

Fiber-Coupled Rotating Two-Photon Light-Sheet Microscopy for Physiological Vestibular Imaging in Larval Zebrafish
Hugo Trentesaux, Geoffrey Migault, Thomas Panier, Georges Debregeas, Volker Bormuth

Scan field rotation with a K-mirror for fast two-photon imaging along curved planes
Shinjini Ghosh, Luca Godenzini, Cécile Telliez, Nikita Vladimirov, Lukas Lüchinger, Yuanzhao Liu, Fritjof Helmchen, Peter Rupprecht

Figure extracted from Ghosh, *et al.* The image is made available under a CC-BY-NC 4.0 International license.

mCranberry: A rationally engineered monomeric red fluorescent protein with 85% quantum yield
Shivam Chaubey, Srijit Mukherjee, Anita Adams, Alice R. Walker, Melonnie L. M. Furgason, Heman Kumar Ramiya Ramesh Babu, Irimpan I. Mathews, Premashis Manna

Data-driven traction force microscopy in 3D collagen hydrogels
Jorge Barrasa-Fano, Laurens Kimps, Alejandro Apolinar-Fernández, Débora Linhares, Iain Muntz, Nele Vaes, Apeksha Shapeti, Elías Núñez-Ortega, Ruth Cardinaels, Gijsje H. Koenderink, José Antonio Sanz-Herrera, Hans Van Oosterwyck

Network fixation expansion microscopy
Yixi Liu, Chi Zhang, Corban Swain, Edward S. Boyden

Figure extracted from Liu, *et al.* The image is made available under a CC-BY 4.0 International license.

GENIE: a multi-agent system for closed-loop autonomous microscopy
Wilson Nieves Vasquez, Jun Lin, Joshua Azukas, Evan Yang, Chi-Kuo Hu, Tengfei Ma, Lina Carlini

SPEx: Compartment-Resolved Proteomics via Expansion Microscopy–Guided Microdissection
Curdin A. Franziscus, Alexia Ferrand, Oliver Biehlmaier, Alexander Schmidt, Anne Spang

Physics-driven self-supervised learning for quantitative high-fidelity structured illumination microscopy
Yujun Tang, Zewei Luo, Xi Zhu, Wenyi Wang, Xichuan Ge, Meiqi Li, Cong Chen, Tongsheng Chen, Ceshi Chen, Peng Xi, Gang Wen

Figure extracted from Tang, *et al.* The image is made available under a CC-BY-NC 4.0 International license.

Fluorescent nanodiamond phantoms for spatial resolution benchmarking in two- and three-photon microscopy
Filip Janiak, Michael Forsthofer, Jakub Czubek, Sinzi Pop, Yangting Fu, Lucia Prieto-Godino, Hans-Ulrich Fried, Małgorzata Szczerska, Tom Baden

BrightEyes-Scope: A Reference Implementation for Image Scanning Microscopy with SPAD Array Detection
Laurent Le, Alessandro Zunino, Eli Slenders, Andrea Bucci, Mattia Donato, Giuseppe Vicidomini

Fully Two-Photon-Driven RESOLFT Microscopy for Super-Resolution Imaging inside Tissue
Ryohei Ozaki-Noma, Hirokazu Ishii, Tetsuichi Wazawa, Joe Sakamoto, Yuichi Kozawa, Yuta Kato, Eri Mukai, Tomomi Nemoto, Takeharu Nagai

Mass Spectrometry Imaging of Caenorhabditis elegans with Fluorescence Microscopy of Tissue-Specific Reporters and Oriented Cryo-Sectioning
R. Einar Jacobson, Elizabeth Wanchisn Smith, Yasuaki Saitoh, Tian (Autumn) Qiu

Plunge freezing tweezers with ultrasonic excitation for reducing preferred particle orientation in cryo-EM
Jakub Wenz, Mischa Flór, Constantin R. Krüger, Marcel Drabbels, Ulrich J. Lorenz

De Novo Design of Orthogonal Far-Red, Orange, and Green Fluorophore-binding Proteins for Multiplexed Imaging
Long Tran, Steffen Klein, David Juergens, Shajesh Sharma, Justin Decarreau, Gyu Rie Lee, Yujia Wang, Wei Chen, Asim K. Bera, Alex Kang, Jon Woods, Emily Joyce, Dionne K Vafeados, Nicole Roullier, Xinting Li, Bingxu Liu, Yang Bo, Edin Muratspahić, Tim A. Brown, Jonathan B. Grimm, Ronak Patel, Luke D. Lavis, Julia Mahamid, Linna An, David Baker

Figure extracted from Tran, *et al.* The image is made available under a CC-BY 4.0 International license.

Ultrastructural comparison of fixation and cryopreservation methods for brain preservation
Alexander German, Cassandra Flügel-Koch, Friedrich Paulsen, Jürgen Winkler, Andrew T. McKenzie

Cryo-tides: synthetic peptides for cryo-EM grid preparation of multi-subunit protein complexes sensitive to the air-water interface
Rose Young, Amy J. S. McGeoch, Matthew Jessop, Basil J. Greber, Claudio Alfieri

A chemigenetic fluorescence lifetime-based biosensor for imaging of ERK activity
Elias Dressler, Rohan S. Eapen, Dennis Pellanda, Yixin Zhang, Jérôme Julmi, Musadiq A. Bhat, Tommaso Patriarchi, Darren Gilmour, Michelle S. Frei

Super-resolution imaging flow cytometry
Yingdong Luo, Tianben Ding, Yuhong Liu, Yaqi Zhao, Hanqing Wang, Masako Nishikawa, Takamasa Ishino, Yosuke Togashi, T. Nicolai Siegel, Keisuke Goda

RhoBAST-FLIM enables high-fidelity and lifetime-assisted super-resolution RNA imaging
Xiao-Xiao Chen, Berkan Bozkurt, Murat Sunbul

Figure extracted from Chen, *et al.* The image is made available under a CC-BY 4.0 International license.

High-throughput 3D super-resolution ultrasound imaging
Weisong Zhao, Nanchao Wang, Zhenqian Han, Xining Xu, Xiangyu Ma, Tianhua Zhou, Jiahui Gui, Yuzhen Liu, Qianbo Liu, Liying Qu, Wenhao Liu, Xiangyan Ding, Xin Liu, Dean Ta, Jiubin Tan, Liangyi Chen, Haoyu Li

Design and Evolution of an Orthogonal HaloTag for Multiplexed Labeling in Cells
Benjamin J. Goldberg, Bryan J. Lampkin, Alexander T. Stead, Siena Stanten, Patrick Rabe, Joshua A. Kritzer

Cortex-wide single-cell activity mapping in freely moving mice
Changliang Guo, Mian Xie, Guohua Qiu, Jian Lu, Yuzhen Liu, Liying Qu, Yuanyuan Huang, Zhenran Guo, Jing Tian, Jingren Lin, Baoyi Zhang, Xuefei Zhang, Junjie Zhao, Xiang Liu, Haochen Long, Jingyi Ma, Bo Zhou, Xianxin Ye, Pingping Zhao, Jingjie Cao, Zhengan Lin, Zhimiao Zhang, Weijie Deng, Jian Wang, Wei Wu, Junwen Wang, Xiaohong Peng, Shiqun Zhao, Shuai Na, Haoyu Li, Wenhao Liu, Qiang Fu, Zengcai V. Guo, Weisong Zhao, Liangyi Chen