Microscopy preprints – new tools and techniques in imaging

Posted by FocalPlane, on 15 May 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!

OptiFoot: a method for recording protein footprints on DNA for microscopy and sequence analysis
Ruta Gerasimaite, Jonas Bucevicius, Dovile Bubnyte, Tanja Koenen, Grazvydas Lukinavicius

Glycan Painting: Triplex Lectin Staining Enables Visualization of Cell-Type-Specific Glycan Profiles in Tissue Sections
Akira Nagasaki

A simplified High-Pressure Freezing Workflow in Autogrids
Miriam S. Weber, Till Epprecht, Jingwei Xu, Gregor L. Weiss

On-lamella super-resolution cryo-CLEM for cryo-ET enabled by vacuum-free ultra-stable cryogenic fluorescence microscopy
Julian Falckenhayn, Vi Quint Duong, Neeraj Prabhakar, Iain Harley, Enoch Lok Him Yuen, Tolga O. Bozkurt, Stephen D. Carter, Vojtěch Pražák, Rainer Kaufmann

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

A stable cryogenic fluorescence microscope for correlative super-resolution light and electron microscopy
Soheil Mojiri, Joseph M. Dobbs, Ricardo Sánchez Loayza, Anna Kreshuk, Julia Mahamid, Jonas Ries

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

Concordant transcriptional and morphological remodeling revealed by in vivo Perturb-CLEAR
Boli Wu, Sean K. Simmons, Seoyeon Kim, Jiwen Li, Masood A. Akram, Chang Sin Park, Xinhe Zheng, Iain Mendez, Sasha Patel, Alan Chau, Nadia Burciu, Pranay Dayal, Thokozile Nyasulu, Nhan Huynh, Grace S. Clarke, X. William Yang, Joshua Z. Levin, Xin Jin

Quantitative imaging of calcium dynamics with a green fluorescent biosensor and fluorescence lifetime imaging
Andrea Caldarola, Sebastián Palacios Martínez, Joachim Goedhart

A StayGold-based calcium ion indicator
Ikumi Miyazaki, Kelvin K. Tsao, Takuya Terai, Kei Takahashi-Yamashiro, Robert E. Campbell

Versatile and Scalable Reflective Micromirrors for Single-Objective Light Sheet Microscopy
Nahima Saliba, Siyang Cheng, Prakash Joshi, Anna-Karin Gustavsson

Adapting Upright Light Sheet Fluorescence Microscopy for Imaging at Air-Liquid Interface
Chad M. Hobson, Kenji Izumi, Jesse S. Aaron, Navaneetha Krishnan Bharathan, M. Fernanda Ceriani, William Giang, Juan I. Ispizua, Andrew P. Kowalczyk, Rachel M. Lee, E. Angelo Morales, Owen F. Puls, Ellen Quarles, Micaela Rodriguez-Caron, Sara N. Stahley, Francisco Tassara, Shaohe Wang, Shunze Yao, Takanori Tsuchiya, Teng-Leong Chew

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

Comprehensive BioImaging Study of the Red Permanent Marker Ink: Re-purposing for Cells Imaging Including Cytoplasmic Membrane Visualization and Comparison with Rhodamine 6G, Deep Red Cell Mask, and DiBAC⋆
Anna A. Abelit, Natalia A. Boitsova, Liudmila E. Yakovleva, Anton A. Kornev, Daniil D. Stupin

Photon-Resolved Excitation-Denoised (PRED) Three-Photon Imaging Improves Detection of Neuronal Activity in Awake and Behaving Mice
Tiberiu S. Mihaila, Eunji Kong, Adrian Negrean, Tristan Geiller, Darcy S. Peterka, Attila Losonczy

Volumetric Scattering Microscopy
Zijun Gao, Keyi Han, Zhi Ling, Hongmanlin Zhang, Edward A Botchwhey, Wen-hao Liu, Xuanwen Hua, Shuyi Nie, Shu Jia

Space-Time Light-Sheet Microscopy
Jinming Zhang, Haokun Luo, Diana M. Mitchell, Shirley Luckhart, Mercedeh Khaja-vikhan, Ayman F. Abouraddy, Demetrios N. Christodoulides, Andreas E. Vasdekis

Polarization-engineered aberration-resilient light sheet microscopy
Yuqing Qiu, Juncheng Zhang, Christopher R Warren, Sara Kacmoli, Vanessa Gonzalez, Cullen B Young, Mengyang J Li, Fei Liu, Kevin Keomanee-Dizon, Rebecca D Burdine, Tian-Ming Fu

Cryo-EM as latent structural landscape microscopy
Haizhao Dai, Qihe Chen, Lingqi Li, Yingjun Shen, Zhenyang Xu, Minzhang Li, Yufan Xie, Jingjing Zheng, Zhijie Liu, Liping Sun, Yuan Pei, Jiakai Zhang, Jingyi Yu

Spatially patterned, spectral single-molecule microscopy
Joseph S. Beckwith, Brendan Cullinane, Daniel F. Heraghty, Sina Krokowski, Caroline L. Jones, Shengbo Yang, Rebecca C. Gregory, R. Andres Floto, Ana Mafalda Santos, Simon J. Davis, Michele Vendruscolo, David Klenerman, Viv Lindo, Praveen Kallamvalliillam Sankaran, Steven F. Lee

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

Mapping 3D tissue orientation with tensor-augmented light-sheet microscopy
Mario Corral-Bolaños, Piyush Swami, Hanna Vila-Merkle, João Lima, Silja P. Vange, Christophe Destrieux, Cyril Poupon, Jessica Pingel, Sanne S. Kaalund, Lídia Bardia, Hans Martin Kjer, Marco Pizzolato, Jeppe Revall Frisvad, Julien Colombelli, Tim B. Dyrby

Superresolution imaging of live samples by centroid reassignment microscopy
Chuan Li, Quan Le, Julian O. Kimura, Bingying Zhao, Yunzhe Li, Jian Zhao, Thomas Bifano, Brandon Weissbourd, John T. Ngo, Jerome Mertz

Spectroscopic DNA-PAINT for simultaneous multiplexed super-resolution microscopy
Md Abul Shahid, Kripa Patel, David A. Miller, Yang Zhang

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

Quantifying optical sectioning in reflection microscopy with patterned illumination
Cathie Ventalon, Agathe Nidriche, Delphine Débarre

Real-time feedback control microscopy for automation of optogenetic targeting
Lucien Hinderling, Alex E. Landolt, Benjamin Grädel, Laurent Dubied, Cédric Zahni, Moritz Kwasny, Dario Bassi, Agne Frismantiene, Talley Lambert, Maciej Dobrzyński, Olivier Pertz

Triplet tumbling microscopy enables in situ quantification of protein complex assembly and dynamics
Julia R. Lazzari-Dean, Alfred Millett-Sikking, Prashant Rao, Zena D. Jensvold, Hannah Baddock, Maria Ingaramo, Aaron H. Nile, Andrew G. York, Magdalena Preciado-López

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

3D-PAULM: Integrated Photoacoustic Tomography and Ultrasound Localization Microscopy for Multiparametric Brain and Tumor Imaging
Yirui Xu, Rui Yao, Huaxin Sheng, Nanchao Wang, Xinyuan Yu, Xueyi Cai, Jiaji Cai, Jinhuan Luo, Jingting Li, Wei Yang, Pengfei Song, Vladislav V. Verkhusha, Junjie Yao

Self-blinking dye restores efficient use of nanobodies in single-molecule localization microscopy
Samrat Basak, Kaushik Inamdar, Yoav G. Pollack, László Albert, Daniel C. Jans, Stefan Jakobs, Jörg Enderlein, Roman Tsukanov, Felipe Opazo

Compressive axial-integrated planar scanning (CAPS) microscopy for high-speed volumetric imaging of cardiac dynamics
Xinyuan Zhang, Jichen Chai, Yi Gong, Milad Almasian, Jonathan Aaron Brewer, Alireza Saberigarakani, Jianqing Jia, Alyssa Hines, Kelli J Carroll, Yifei Lou, Yichen Ding

Simulating Multi-Colour Single-Molecule Localisation Microscopy Using an RGB Camera
Ava E D Kelly, John S H Danial

Multiscale Light Field Microscopy Platform for Multi-purpose Dynamic Volumetric Bioimaging
Yangyang Bai, Matt Jones, Lauro Sebastian Ojeda, Janielle Cuala, Lynne Cherchia, Senta K. Georgia, Scott E. Fraser, Thai V. Truong

Direct Membrane Penetration of Oligoarginines by Fluorescence and Cryo-electron Microscopy Combined with Molecular Simulations
Katarína L. Baxová, Mattia I. Morandi, Nadav Scher, Patrik Kula, Ondrej Tichacek, Itay Schachter, Petro Busko, Jiri Zahradnik, Mario Vazdar, Jovi Koikkara, Christoph Allolio, Ori Avinoam, Pavel Jungwirth

Doubling the Field of View in Common-Path Digital Holographic Microscopy via Wavelength Scanning and Polarization Gratings
Aleksandra Piekarska, Mikołaj Rogalski, Marzena Stefaniuk, Maciej Trusiak, Piotr Zdańkowski

Repetition-controllable gain-managed nonlinear fiber amplifier enables ultrashort, multiphoton imaging with reduced photodamage
James Read, Duanyang Xu, Jikun Yan, Andrew Rawlings, Siddhi Chugh, Mirella Cosma Spalluto, Paul Elkington, Janos M. Kanczler, Simon I.R. Lane, Sumeet Mahajan, Lin Xu

Cryo-FIB lamellae enable ultra-high excitation laser intensities for cryogenic super-resolution fluorescence imaging
Soheil Mojiri, Joseph M. Dobbs, Jenny Sachweh, Nestor Castillo, Jonas Ries, Julia Mahamid

Counting fluorescent emitters with a single photon avalanche diode array
Clayton Seitz, Carmella Evans-Molina, Jing Liu

Non-covalent reversibly photoconvertible fluorescent tags for wash-free protein labeling
Mrinal Mandal, Yuriy Shpinov, Alienor Lahlou, Fivos Pham, Lina El Hajji, Ian Coghill, Eve Laureau, Marie-Aude Plamont, Franck Perez, Thomas Le Saux, Isabelle Aujard, Arnaud Gautier, Ludovic Jullien

Quantitative evaluation of LED based optical autofocus module
S. Habte, S. Kumar, J. Lightley, E. Garcia, M.A.A. Neil, P.M.W French

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

Light-sheet excitation-encoded volumetric spectroscopy for fast multiplexed imaging and quantitative physicochemical mapping in cells
Jinhong Yan, Jiankai Xia, Jiayi Liu, Yi He, Jeongmin Kim, Kun Chen

A CandiChrome toolkit for multicolor labeling of Candida cells
Cai-Ling Ke, Jingcheng Xu, Corey Frazer, Richard J. Bennett

Structure-guided, physics-aware reconstruction expands scan-limited multiphoton imaging
Shoupei Liu, Yaoguang Zhao, Jiahao Hu, Yanfeng Zhu, Huiyun Yu, Bo Li

Kinetic and Mechanistic Characterization of RSpFAST, A Non-Covalent Versatile Chemogenetic Platform for Fluorescence Imaging
Yuriy Shpinov, Mrinal Mandal, Vincent van Deuren, Alienor Lahlou, Matthias Le Bec, Raja Chouket, Chaima Hadj Moussa, Clara Bonin, Hessam Sepasi Tehrani, Ian Coghill, Lina El Hajji, Karim Ounoughi, Jaime Franco Pinto, Marie-Aude Plamont, Philippe Pelupessy, Isabel Ayala, Franck Perez, Isabelle Aujard, Thomas Le Saux, Arnaud Gautier, Peter Dedecker, Bernhard Brutscher, Ludovic Jullien

Two-photon characterisation of long-Stokes-shift dye ATTO 490LS for single-laser multicolour imaging
King Yee Cheung, Yue Wu, Shu Ying Lee, Xianyuan Zhang, Masahiro Fukuda, Danesha Devini Suresh, Adam Claridge-Chang

Altair-dvOPM: an open-access platform for large-field three-dimensional tissue imaging
Tai Ngo, Muaaz Faiyazuddin, Trung Duc Nguyen, John Haug, Qionghua Shen, Seweryn Gałecki, Hazel M. Borges, Bingying Chen, Xiaoding Wang, Hao Zhu, Samuel S. Pappas, Fabian F. Voigt, Reto Fiolka, Kevin M. Dean

DNA-Functionalized Nanoparticles for Multicolor Cathodoluminescence Imaging
Jeremy B. Conway, Sohaib Abdul Rehman, Maxim B. Prigozhin

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

Physics-informed self-supervised learning enables spectra-free multiplexed imaging on standard fluorescence microscopes
Jiankai Xia, Jinhong Yan, Mingxuan Tang, Bin Zhao, Kun Chen

PIB: Parallel ion beam etching of sections collected on wafer for ultra large-scale connectomics
Hongtu Ma, Yanan Lv, Minggang Wang, Zhuangzhuang Zhao, Jing Liu, Xiaohui Dong, Yanchao Zhang, Jinyue Guo, Bohao Chen, Lina Zhang, Sheng Chang, Haoran Chen, Hao Zhai, Linlin Li, Xi Chen, Hua Han

Simultaneous plane illumination and detection in confocal microscopy using a mode-selective photonic lantern
Rodrigo Itzamná Becerra-Deana, Simon Desrochers, Raphaël Maltais-Tariant, Simon Brais-Brunet, Guillaume Ramadier, Stéphane Virally, Lucien E. Weiss, Caroline Boudoux

Super-Resolution Structured-Illumination X-Ray Microscopy based on Fourier Decomposition
Stefan Schwaiger, Lennart Forster, Martin Dierolf, Franz Pfeiffer, Benedikt Günther