Microscopy preprints – new tools and techniques in imaging

Posted by FocalPlane, on 22 October 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!

Multi-immersion Oblique Plane Microscope (miOPM): A reconfigurable platform for high-resolution Light-Sheet Fluorescence Microscopy
Bingying Chen, Alfred Millett-Sikking, Seweryn Gałecki, Stephan Daetwyler, Jenny Jiou, Jim Monistrol, Qionghua Shen, Felix Zhou, Hsin-Yu Lin, Edward Jenkins, Miriam C. Stein, Madeleine Marlar-Pavey, Gabriel Sturm, Alexander L. Li, Qiaosi Tang, Brian Feng, Ulises Diaz, Yannan Chen, Ary Shalizi, Astrid Gillich, Jonathan R. Friedman, Raju Tomer, Bo-Jui Chang, Wallace F. Marshall, Sarah Shahmoradian, Kevin M. Dean, Reto Fiolka

Identification of optimal fluorophores for use in the Drosophila embryo
Bernardo Chapa-y-Lazo, Thamarailingam Athilingam, Prabhat Tiwari, Prachi Pathak, Shaobo Zhang, Sophie Theis, Timothy E Saunders

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

A versatile microfluidics platform for enhanced multi-target super-resolution microscopy
Samrat Basak, Kim Chi-Vu, Nikolaos Mougios, Nazar Oleksiievets, Yoav Pollack, Sören Brandenburg, Felipe Opazo, Stephan E. Lehnart, Jörg Enderlein, Roman Tsukanov

Smart Microscopy: Current Implementations and a Roadmap for Interoperability
Lucien Hinderling, Hannah S. Heil, Alfredo Rates, Philipp Seidel, Manuel Gunkel, Benedict Diederich, Thomas Guilbert, Rémy Torro, Otmane Bouchareb, Claire Demeautis, Célia Martin, Scott Brooks, Evangelos Sisamakis, Erwan Grandgirard, Jerome Mutterer, Harrison Oatman, Jared Toettcher, Andrii Rogov, Nelda Antonovaite, Karl Johansson, Johannes K. Ahnlinde, Oscar André, Philip Nordenfelt, Pontus Nordenfelt, Claudia Pfander, Jürgen Reymann, Talley Lambert, Marco R. Cosenza, Jan O. Korbel, Rainer Pepperkok, Lukas C. Kapitein, Olivier Pertz, Nils Norlin, Aliaksandr Halavatyi, Rafael Camacho

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

An accessible microfluidic perfusion platform for time-restricted control of zebrafish embryonic patterning
Mohammed Nakhuda, M. Fethullah Simsek

Single-aperture SLAM microscopy with amplitude-tailored vector beams
Jeffrey Demas, Iván Coto Hernández, J. Matthew Dubach, Siddharth Ramachandran

Low-Cost 3D Printed Optics for Super-Resolution Multifocal Structured Illumination Microscopy
Jay Christopher, Liam M. Rooney, Charlie Butterworth, Gail Mcconnell, Ralf Bauer

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

Radiation dose effects in correlative X-ray / cryo-electron microscopy of frozen hydrated biological samples
Thorsten B. Blum, Vincent Olieric, Ana Diaz, Takashi Ishikawa, Volodymyr M. Korkhov

Maximising imaging volumes of expanded tissues for inverted fluorescence microscopy
Miguel Cardoso Mestre, Jacob R. Lamb, Madeline A. Lancaster, James D. Manton

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

Ballistic Microscopy (BaM)
A. S. Jijumon, Ray Chang, Manu Prakash

Parallel frequency-multiplexed aberration measurement for widefield fluorescence microscopy
Hyeonggeon Kim, Iksung Kang, Ryan Natan, Na Ji

Dual-color expansion microscopy of membrane proteins using bioorthogonal labeling
Steven Edwards, Birthe Meineke, Sebastian Bauer, Hans Blom, Simon Elsässer, Hjalmar Brismar

Single-aperture SLAM microscopy with amplitude-tailored vector beams
Jeffrey Demas, Iván Coto Hernández, J. Matthew Dubach, Siddharth Ramachandran

Broadband electronic resonance coherent anti-Stokes/Stokes Raman scattering microscopy
Yusuke Murakami, Norihide Sagami, Minori Masaki, Ryosuke Oketani, Masashi Yanagisawa, Hideaki Kano, Sakiko Honjoh, Kotaro Hiramatsu

Exploring the potential for scanning electron microscopy/focused ion beam-based diffraction for screening cryo-transmission electron microscopy samples
Eric V. Woods, Christoph Wigge, Yujun Zhao, René de Kloe, Tim M. Schwarz, Ben Britton, Stefan Zaefferer, Baptiste Gault

SIMple: A fibre-based platform for accessible structured illumination microscopy
Rebecca M. Mcclelland, Edward N. Ward, Francesca W. van Tartwijk, Stephen Devlin, Junqing Wang, Clemens F. Kaminski

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

Longitudinal Assessment of Fluorescence Stability Shows Fluorescence Intensity Decreases Over Time: Implications for Fluorescence Microscopy Studies
Sean C Sweat, Sarah P.R. Berg, Tenzin Kunkhyen, Emma G Foster, Claire E J Cheetham

Seeing in the Dark: Intelligent Fourier Light Field Imaging for Bioluminescence Microscopy
Luis-Felipe Morales-Curiel, Michael Krieg

Interface-Sensitive Epi-Coherent Anti-Stokes Raman Scattering Microscopy for Imaging Cell Adhesion Dynamics
Mingmin Zhou, Bin Dong, Laura Lukov, Seohee Ma, Xinyi He, Chi Zhang

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

Radiation dose effects in correlative X-ray / cryo-electron microscopy of frozen hydrated biological samples
Thorsten B. Blum, Vincent Olieric, Ana Diaz, Takashi Ishikawa, Volodymyr M. Korkhov

Microbubble Backscattering Intensity Improves the Sensitivity of Three-dimensional (3D) Functional Ultrasound Localization Microscopy (fULM)
YiRang Shin, Qi You, Yike Wang, Matthew R. Lowerison, Bing-Ze Lin, Pengfei Song

Interferometric Image Scanning Microscopy for label-free imaging at 120 nm resolution inside live cells
Michelle Küppers, W. E. Moerner

Super-resolved live imaging of thick biological samples with 3D Random Illumination Microscopy (3D-RIM)
Thomas Mangeat, Lorry Mazzella, Benoît Rogez, Guillaume Giroussens, Xiangyi Li, Mathilde Bernard, Pablo Vargas, Marc Allain, Simon Labouesse, Jérôme Idier, Loïc LeGoff, Anne Sentenac

A nanobody-gold conjugate for the detection of GFP-tagged synaptic proteins by dual light-electron microscopy
Charles Ducrot, Cécile Lemoigne, Paul Lecompte Saint-Jean, Tiffany Cloâtre, Sophie Daburon, Kerstin Seiling, Leonie Mohrmann, Astrid Rohlmann, Markus Missler, Rémi Fronzes, Daniel Choquet, Matthieu Sainlos, Olivier Thoumine

A correlative quantitative phase contrast and fluorescence super-resolution microscope for imaging molecules in their cellular context
Yujin Bao, Zach Marin, Xiongchao Chen, Qiong Liu, Yazgan Tuna, Sylvi Stoller, Florian Schueder, Chuyue Zhang, Suet Yin Sarah Fung, Min Wu, Karla M. Neugebauer, Jonathon Howard, Chi Liu, David Baddeley, Michael Shribak, Joerg Bewersdorf

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

Determination of factors that allow cryogenic nanoscopy with high power illumination without devitrification
Jan Huebinger, Philippe I.H. Bastiaens

Bridging the resolution gap in cryo-CLEM by introducing cryo-SXT: cryo-CLXEM
Johannes Groen, Anastasia Gazi, Sergey Kapishnikov, Anne Brelot, Matthijn Vos, Jost Enninga, Eva Pereiro, Anna Sartori-Rupp

Offsetting ROS-mediated arrest of endothelial fenestration dynamics permits long-term optical super-resolution- and AFM-imaging
Annika Kiel, Marcin Luty, Angela Kralemann-Köhler, Laureen Patricia Helweg, Jasmin Schürstedt-Seher, Jerzy Kotlinowski, Jakub Pospíšil, Malgorzata Lekka, Thanh-Diep Ly, Thomas Huser, Jan Schulte am Esch, Wolfgang Hübner, Karolina Szafranska, Bartlomiej Zapotoczny

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

Overcoming Preferred Orientation in Cryo-EM With Ultrasonic Excitation During Vitrification
Harry M. Williams, Wyatt A. Curtis, Michal Haubner, Jakub Hruby, Marcel Drabbels, Ulrich J. Lorenz

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

Fast Hyperspectral and Super-Resolved Mapping of Lipid Membrane Polarity with Single-Molecule Sensitivity
Elric Dion Pott, Meek Yang, James Ethan Batey, Joie Embree, Bin Dong

Maskless and on-chip LED-array microscope with spatially-varying angle calibration for centimeter-scale phase imaging
Sibi Chakravarthy Shanmugavel, Vindya Senanayake, Donghwa Suh, Jeffrey M. Gross, Shwetadwip Chowdhury

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

Label-Free, Real-Time, In Vivo Optical Biopsy with a Handheld Quantitative Phase Microscope
Zhe Guang, Srinidhi Bharadwaj, Zhaobin Zhang, Stewart Neill, Jeffrey J. Olson, Francisco E. Robles

High Throughput Hyperspectral and Multiplexed Super-Resolution Fluorescence Imaging by SP-STORM
Elric Dion Pott, Meek Yang, James Ethan Batey, Joie Embree, Bin Dong

A 40 MHz femtosecond laser repetition frequency divider for enhanced two-photon imaging
Shiming Tang

SBIS, a new orange fluorescent vital probe for the 4D imaging of brown algal cells
Marie Zilliox, Mayeul Collot, Bénédicte Charrier

Deep3DSIM: Super-resolution imaging of thick tissue using 3D 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

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

Shadow montage and cone-beam reconstruction in 4D-STEM tomography
Shahar Seifer, Lothar Houben, Michael Elbaum

Alternating Angle Milling Suppresses Streaking Artifacts in FIB-SEM Imaging
Gleb Shtengel, Wei Qiu, Jesse Aaron, Arthur S. Crowe, Alexey A. Polilov, Katerina Karkali, Christopher K.E. Bleck, Harald H. Hess

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

A non-toxic, user-friendly buffer that enhances green fluorophore performance in conventional and super-resolution imaging
Anaïs C. Bourges, Mathias Marcos de Vargas, Azevedo, Viktorija Glembockyte, Robin Van den Eynde, Wim Vandenberg

Cryoprotectants-assisted plunge freezing of thick brain tissue specimens for targeted physiologically relevant cryo-imaging in situ
Ash Weier, Louis Perez, Fei Gao, Elliot T. Morgan, Pingting Liu, Ivan C. Mounteer, Garry P. Morgan, Qian Shi, Fabio A. Vigil, Lydia-Marie Joubert, Andreas Hoenger, Michael H. B. Stowell, Oleg Klykov

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

Fluid-Squid: DIY Multiplexed Imaging of Cells and Tissues
John W. Hickey, Hongquan Li, Chiara Caraccio, You Yan, Kevin Marx, Peter Martin, Hope T Leng, John Fayiah, Elvis Towalid, Bonnie Dighero-Kemp, Garry P. Nolan, Manu Prakash, David R. McIlwain

Massively Parallel Bead-Free Force Spectroscopy with Fluorescence
Adam B. Yasunaga, Ryan Riopel, David t. R. Bakker, Dyuti Raghu, Micah Yang, Isaac T. S. Li

Correlative MS Imaging for cellular identification and analysis of in situ cryo-ET
Andre Schwarz, Jakob Meier-Credo, Arne Behrens, Jürgen Reichert, Lea Dietrich, Erin M. Schuman, Julian D. Langer

“QuickStainer”: a rapid negative staining device for improved preservation of molecular structure
Vu Nguyen, Ruchi Gautam, Arun Kumar Somavarapu, Debabrata Dutta, Aditya Patra, Jinghua Ge, Christopher M. Yengo, Raúl Padrón, Roger Craig

Preservation of soluble enhanced green fluorescent protein (EGFP) within fixed NIH 3T3 fibroblasts
John T. Elliott, Mahir Mohiuddin, Alex Tona

Logic-gating the HaloTag system with Conditional-Halo-ligator ‘CHalo’ reagents
Philipp Mauker, Carmen B.J. Zecha, Lucas Dessen-Weissenhorn, Luciano Román-Albasini, Joyce C.M. Meiring, Julia I. Brandmeier, Daniela Beckmann, Jan P. Prohaska, Martin Reynders, Yi Louise Li, Kristina Mrug, Hannah von Schwerin, Nynke A. Vepřek, Julia F. Gaisbauer, Leif Dehmelt, Perihan Nalbant, Jennifer Zenker, Anna Akhmanova, Martin Kerschensteiner, Angelika B. Harbauer, Julia Thorn-Seshold, Oliver Thorn-Seshold