Microscopy preprints – new tools and techniques in imaging

Posted by FocalPlane, on 21 March 2025

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!

Ångström-resolution imaging of cell-surface glycans
Luciano A. Masullo, Karim Almahayni, Isabelle Pachmayr, Monique Honsa, Larissa Heinze, Sarah Fritsche, Heinrich Grabmayr, Ralf Jungmann, Leonhard Möckl

Lattice light sheet activation structured illumination volumetric super-resolution live microscopy
Dong Li, Xue Dong, Quan Meng, Xiaoyu Yang, Haoyu Chen, Chang Qiao, Yuhuan Lin, Siwei Zhang, Xiaohan Geng, Linghui Luan, Tao Jiang, Wenfeng Fu, Amin Jiang, Wencong Xu, Jiabao Guo, Rongfei Wei

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

Spectral STED microscopy improves spectral sensitivity with polarity-sensitive probes and enables correlative measurements of membrane order and anomalous lipid diffusion
Iztok Urbančič, Falk Schneider, Silvia Galiani, Erdinc Sezgin, Christian Eggeling

SparseFocus: Learning-based One-shot Autofocus for Microscopy with Sparse Content
Yongping Zhai, Xiaoxi Fu, Qiang Su, Jia Hu, Yake Zhang, Yunfeng Zhou, Chaofan Zhang, Xiao Li, Wenxin Wang, Dongdong Wu, Shen Yan

AI-assisted protein design to rapidly convert antibody sequences to intrabodies targeting diverse peptides and histone modifications
Gabriel Galindo, Daiki Maejima, Jacob DeRoo, Scott R. Burlingham, Gretchen Fixen, Tatsuya Morisaki, Hallie P. Febvre, Ryan Hasbrook, Ning Zhao, Soham Ghosh, E. Handly Mayton, Christopher D. Snow, Brian J. Geiss, Yasuyuki Ohkawa, Yuko Sato, Hiroshi Kimura, Timothy J. Stasevich

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

Development of a BiAD sensor for locus-specific detection of cellular histone acetylation dynamics by fluorescence microscopy
Anja R. Köhler, Nicole Gutekunst, Annika Harsch, Pavel Bashtrykov, Albert Jeltsch

Direct-view oblique plane microscopy
Jacob R. Lamb, Miguel Cardoso Mestre, Madeline Lancaster, James D. Manton

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

Cryosectioning-enhanced super-resolution microscopy for single-protein imaging across cells and tissues
Johannes Stein, Maria Ericsson, Michel Nofal, Lorenzo Magni, Sarah Aufmkolk, Ryan B. McMillan, Laura Breimann, Conor P. Herlihy, S. Dean Lee, Andréa Willemin, Jens Wohlmann, Laura Arguedas-Jimenez, Peng Yin, Ana Pombo, George M. Church, Chao-ting Wu

High Spatiotemporal Resolution Structured Illumination Microscopy: Principle, Instrumentation, and Applications
Han Wang, Wenshu Wang, Xinzhu Xu, Meiqi Li, Peng Xi

SMILE: a universal tool for modulated-enhanced localization microscopy to achieve minimal three-dimensional resolution
Hongfei Zhu, Yile Sun, Xinxun Yang, Enxing He, Lu Yin, Hanmeng Wu, Mingxuan Cai, Yubing Han, Renjie Zhou, Cuifang Kuang, Xu Liu

Visualizing sub-organellar lipid distribution using correlative light and electron microscopy
H. Mathilda Lennartz, Suman Khan, Kristin Böhlig, Weihua Leng, Falk Elsner, Nadav Scher, Michaela Wilsch-Bräuninger, Ori Avinoam, André Nadler

Optochemical control over mRNA translation by photocaged phosphorodiamidate morpholino oligonucleotides in vivo
Katsiaryna Tarbashevich, Atanu Ghosh, Arnab Das, Debajyoti Kuilya, Swrajit Nath Shrama, Surajit Sinha, Erez Raz

Shallow-angle intracranial cannula for repeated infusion and in vivo imaging with multiphoton microscopy
Steven S. Hou, Joyce Yang, Yeseo Kwon, Qi Pian, Yijing Tang, Christine A. Dauphinais, Maria Calvo-Rodriguez, Mirna El Khatib, Sergei A. Vinogradov, Sava Sakadzic, Brian J. Bacskai

Isotropic, aberration-corrected light sheet microscopy for rapid high-resolution imaging of cleared tissue
Mostafa Aakhte, Gesine F. Müller, Joe Li, Kurt R. Weiss, Lennart Roos, Aleyna M. Diniz, Jan Wenzel, Markus Schwaninger, Tobias Moser, Jan Huisken

Economical Method to Construct a Prism-based TIRF Setup on an Existing Confocal Microscope to Perform smFRET Experiments
Pratibha Agarwala, Dibyendu K. Sasmal

Glyco-STORM: Nanoscale Mapping of the Cellular Glycosylation Landscape
Helene Gregoria Schroeter, Steffen Sass, Mike Heilemann, Thomas Kuner, Maja Klevanski

Caging-group-free photoactivatable fluorophores with far-red emission
Richard Lincoln, Alexey N. Butkevich, Clara-Marie Gürth, Alena Fischer, Anna R. Emmerich, Maximilian Fidlin, Mariano L. Bossi, Stefan W. Hell

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

Color-neutral and reversible tissue transparency enables longitudinal deep-tissue imaging in live mice
Carl H.C. Keck, Elizabeth L. Schmidt, Richard H. Roth, Brendan M. Floyd, Andy P. Tsai, Hassler B. Garcia, Miao Cui, Xiaoyu Chen, Chonghe Wang, Andrew Park, Su Zhao, Pinyu A. Liao, Kerriann M. Casey, Wencke Reineking, Sa Cai, Ling-Yi Zhang, Qianru Yang, Lei Yuan, Ani Baghdasaryan, Eduardo R. Lopez, Lauren Cooper, Han Cui, Daniel Esquivel, Kenneth Brinson, Xiaoke Chen, Tony Wyss-Coray, Todd P. Coleman, Mark L. Brongersma, Carolyn R. Bertozzi, Gordon X. Wang, Jun B. Ding, Guosong Hong

Real-Time Tracking of Tumor Invasion Dynamics in Organotypic Brain Slices at Subcellular Resolution
Jana B. Petr, Meng-Syuan Lin, Dina Hochuli, Andreas Hierlemann, Martin Baumgartner, Mario M. Modena

Alternate dyes for image-based profiling assays
Suganya Sivagurunathan, Patrick Byrne, Alán F. Muñoz, John Arevalo, Anne E. Carpenter, Shantanu Singh, Maria Kost-Alimova, Beth A. Cimini

SPECTRE-Plex: an automated, fast, high-resolution-enabled approach for multiplexed cyclic imaging and tissue spatial analysis
Michael D. Anderson, Abigail Plone, Jeffrey La, Madison Wong, Krishnan Raghunathan, Jocelyn A. Silvester, Jay R. Thiagarajah

Using Beads as a Focus Fiduciary to Aid Software-based Autofocus Accuracy in Microscopy
Isabel Gibson, Elizabeth Julie Osterlund, Ray Truant

PerfectlyAverage: a classical open-source software method to determine the optimal averaging parameters in laser scanning fluorescence microscopy
Shannan Foylan, Liam M. Rooney, William B. Amos, Gwyn W. Gould, Gail McConnell

Coaxial line-scanning Brillouin microscopy
Chenjun Shi, Jitao Zhang

Luminos: open-source software for bidirectional microscopy
Daniel G. Itkis, F. Phil Brooks III, Hunter C. Davis, Raphael Hotter, J. David Wong-Campos, Yitong Qi, Bill Z. Jia, Madeleine Howell, Marley Xiong, Rebecca Frank Hayward, Byung Hun Lee, Yangdong Wang, Rebecca T. Perelman, Adam E. Cohen

Chiral Single Molecule Localization Microscopy (chiralSMLM)
S Aravinth, Neeraj Pant, Partha P. Mondal

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

Transverse Sheet Illumination Microscopy (TranSIM): A High-Speed Platform for Large-Scale Volumetric Imaging
Javier Carmona, Blake A Madruga, Steve A Mendoza, JY B Jeong, Laurent Bentolila, Katsushi Arisaka

Patterned illumination enables denser deep-learning based single-molecule localization microscopy
Jelmer Cnossen, Shih-Te Hung, Daniel Fan, Josiah B. Passmore, Lukas C. Kapitein, Nynke Dekker, Carlas S. Smith

Fast volumetric fluorescence lifetime imaging of multicellular systems using single-objective light-sheet microscopy
Valentin Dunsing-Eichenauer, Johan Hummert, Claire Chardès, Thomas Schönau, Léo Guignard, Rémi Galland, Gianluca Grenci, Max Tillmann, Felix Koberling, Corinna Nock, Jean-Baptiste Sibarita, Virgile Viasnoff, Ivan Michel Antolovic, Rainer Erdmann, Pierre-François Lenne

Optical sectioning for reflection interference microscopy: quantitative imaging at soft interfaces
Cathie Ventalon, Oksana Kirichuk, Yotam Navon, Yan Chastagnier, Laurent Heux, Ralf P. Richter, Lionel Bureau, Delphine Débarre

An Enhanced Mountain Climbing Search Algorithm to Enable Fast and Accurate Autofocusing in High Resolution Fluorescence Microscopy
Yuetong Jia, Edward N Ward, Francesca W van Tartwijk, Yutong Yuan, Yuqing Feng, Clemens F Kaminski

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

A novel method (RIM-Deep) for enhancing imaging depth and resolution stability of deep cleared tissue in inverted confocal microscopy
Yisi Liu, Pu Wang, Junjie Zou, Hongwei Zhou

Fast in vivo deep-tissue 3D imaging with selective-illumination NIR-II light-field microscopy and aberration-corrected implicit neural representation
Peng Fei, Fenghe Zhong, Xue Li, Mian He, Yihang Huang, Chengqiang Yi, Shiqi Mao, Xin Huang, Kui Ren, Miaomiao Kang, Dong Wang, Zhijun Zhang, Dongyu Li

DNA-PAINT imaging with hydrogel imprinting and clearing
Johannes Stein, Lorenzo Magni, George M. Church

SLICK: A Sandwich-LIke Culturing Kit for in situ Cryo-ET Sample Preparation
Qiuye Li, Li Zhang, Qin Xu, Peng Zhang, Shiwei Zhu

Biological volume EM with focused Ga ion beam depends on formation of radiation-resistant Ga-rich layer at block face
Zijie Yang, Joshua Kim, Cameron M. Baenen, Samuel J. Fulton, Guofeng Zhang, Xiaobing Chen, Maria A. Aronova, Richard D. Leapman

Foam film vitrification for cryo-EM
Yue Zhang, Biplob Nandy, Kasim Sader, Chris Russo, Jan Löwe

Focus-Tunable Two-Photon Fiberscope Enabling in vivo Imaging at Selected Depths
Yuehan Liu, Jiayun L. Huang, Xingde Li

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

The graphene-based affinity cryo-EM grid for the endogenous protein structure determination
Sojin An, Eungjin Ahn, Tyler Koo, Soyoung Park, Boeon Suh, Krishna P. Rengasamy, Gaocong Lyu, Cheal Kim, Byungchul Kim, Hanseong Kim, Sangho Park, Dongyan Tan, Uhn-Soo Cho

Single-molecule validation and optimized protocols for the use of secondary nanobodies in multiplexed immunoassays
Rebecca S. Saleeb, Judi O’Shaughnessy, Ryan Ferguson, Candace T. Adams, Mathew H. Horrocks

A versatile miniature two-photon microscope enabling multicolor deep-brain imaging
Runlong Wu, Chunzhu Zhao, Shan Qiu, Yufei Zhu, Lifeng Zhang, Qiang Fu, Yanhui Hu, Dakun Wu, Fei Yu, Fangxu Zhou, Haipeng Huang, Yunfeng Zhang, Xianhua Wang, Aiming Wang, Heping Cheng

A tripartite chemogenetic fluorescent reporter: design and evaluation for visualizing ternary protein complexes
Sara Bottone, Fanny Broch, Antoine Gedeon, Aurélien Brion, Lina El Hajji, Hela Benaissa, Arnaud Gautier

Broad application of plant protein tagging with ALFA tag for nanobody-based imaging and biochemical approaches
Julie Neveu, Julien Spielmann, Steven Fanara, Charlotte Delesalle, Sylvain Cantaloube, Gregory Vert

Fast Two-photon Microscopy by Neuroimaging with Oblong Random Acquisition (NORA)
Esther Whang, Skyler Thomas, Ji Yi, Adam S. Charles

Bidirectional quantitative scattering microscopy
Kohki Horie, Keiichiro Toda, Takuma Nakamura, Takuro Ideguchi

Generalized reciprocal diffractive imaging for stand-alone, reference-free, fast-measurable quantitative phase microscopy
Jeonghun Oh, Herve Hugonnet, Weisun Park, YongKeun Park

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

Enhancing Deep Learning Based Structured Illumination Microscopy Reconstruction with Light Field Awareness
Long-Kun Shan, Ze-Hao Wang, Tong-Tian Weng, Xiang-Dong Chen, Fang-Wen Sun

Confocal structured illumination microscopy for super-resolution imaging: theory and numerical simulations
Junzheng Peng, Jiahao Xian, Xi Lin, Manhong Yao, Shiping Li, Jingang Zhong

Sample Motion for Structured Illumination Fluorescence Microscopy
Ruiming Cao, Guanghan Meng, Laura Waller

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

Complementary Speckle STED Microscopy
Payvand Arjmand, Samlan Chandran Thodika, Elsa Bivas, Haoyang Li, Martin Oheim, Hiroyuki Yoshida, Etienne Brasselet, Marc Guillon