Microscopy preprints – new tools and techniques in imaging

Posted by FocalPlane, on 3 April 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!

aDISCO: A Broadly Applicable Method for 3D Microscopy of Archival Paraffin-Embedded Human Tissues
Anna Maria Reuss, Peter Rupprecht, Dominik Groos, Martina Cerisoli, Lena Nordberg, Lukas Frick, Fabian F. Voigt, Nikita Vladimirov, Philipp Bethge, Regina Reimann, Fritjof Helmchen, Adriano Aguzzi

Nanobodies equipped with HaloTag variants enable rapid and straightforward one-step immunofluorescence lifetime multiplexing
László Albert, Samrat Basak, Henrike Körner, Nazar Oleksiievets, Nikolaos Mougios, Elena R. Cotroneo, Michelle S. Frei, Jörg Enderlein, Johannes Broichhagen, Nadja A. Simeth, Roman Tsukanov, Felipe Opazo

A green fluorescent protein for live imaging in hyperthermophiles
Yin-Wei Kuo, Arthur Radoux-Mergault, Tom Dubois, Alice Cezanne, Fan Zhang, Pier Andrée Penttilä, Michaela Wagner, Gautam Dey, Sonja-Verena Albers, Buzz Baum

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

Fluorescent organelle markers in Cryptococcus neoformans: a versatile toolkit for live-cell subcellular localization
Yeseul Choi, Yong-Sun Bahn, Joseph Heitman

A non-invasive approach for understanding localized force generation in 3D tissues
Niels Gouirand, Meti Ibrahimi, Claire Valotteau, Brice Lecouffe, Andre Le Bivic, Dominique Massey Harroche, Felix Rico, Matthias Merkel, Delphine Delacour, Elsa Bazellieres

A Lightweight Deep Learning Framework for Fast, Real-Time Super-Resolution Fluctuation Imaging
Miyase Tekpınar, Jelle Komen, Hana Valenta, Ran Huo, Klarinda de Zwaan, Peter Dedecker, Nergis Tomen, Kristin Grußmayer

Fluorogenic speed-optimized DNA-PAINT probes enable super-resolution imaging of whole cells
Sylvi Stoller, Asmita Jha, Joerg Bewersdorf, Florian Schueder

DySTrack: a modular smart microscopy tool for live tracking of dynamic samples on modern commercial microscopes
Zimeng Wu, Octavian Voiculescu, Alessandro Mongera, Roberto Mayor, Mie Wong, Jonas Hartmann

Open Fourier Ptychographic Microscopy (OpenFPM)
Lewis D. Walker, Laura Copeland, Liam M. Rooney, Christopher Bendkowski, Michael Shaw, Gail McConnell

Traction Force Microscopy with DNA FluoroCubes
Armina Mortazavi, Jianfei Jiang, Philip Laric, Dominic A. Helmerich, Rick Seifert, Svetozar Gavrilovic, Markus Sauer, Benedikt Sabass

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

Fiber optical parametric amplification of low-photon-flux microscopy signals
J. Demas, L. Tan, S. Ramachandran

Physics-Informed Self-Supervised Generative Model for 3D Localization Microscopy
Ofri Goldenberg, Tal Daniel, Dafei Xiao, Yael Shalev Ezra, Yoav Shechtman

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

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

Liquid Phase Backscattered Scanning Electron Microscopy of Bacillus subtilis Spores
Jack Bromley, Adrián Pedrazo-Tardajos, Yongqiang Meng, Matthew C. Spink, Dogan Ozkaya, Rodney S. Ruoff, Graham Christie, Angus I. Kirkland, Judy S. Kim

Automated Cyclic Super-Resolution Microscopy for Nanoscale Protein Mapping
Hongqiang Ma, Chaojie Zhang, Shuyuan Zheng, Shengwei Chen, Yang Liu

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

A Modular In-Incubator Microscope for Longitudinal Live Cell Microscopy
Drew Ehrlich, Yohei Rosen, Santhosh Arul, John Minnick, Seth Nicholson, Kateryna Voitiuk, Spencer Seiler, Anna Toledo, Samira Vera-Choqqueccota, Neil Doherty, Jess Sevetson, Max McGlynn, Kivilcim Doganyigit, Maryam Moarefian, Sri Kurniawan, Mohammed A. Mostajo-Radji, Sofie R. Salama, Ethan Winkler, David Haussler, Mircea Teodorescu

Volume and surface methods for microparticle traction force microscopy: a computational and experimental comparison
Simon Brauburger, Bastian Karl Kraus, Tobias Walther, Tobias Abele, Kerstin Goepfrich, Ulrich Sebastian Schwarz

Cost-function Optimized Maximal Overlap Drift Estimation for Single Molecule Localization Microscopy
Lenny Reinkensmeier, Sarah Aufmkolk, Irene Farabella, Alexander Egner, Mark Bates

Diffractive scanning live volumetric two-photon microscopy within the contracting mouse intestine
Jonas Jurkevičius, Milvia Alata, Moritz Wiggert, Maximilian Rixius, Stefan Reinhards, Matthea Thielking, Christian Stock, Candice Fung, Alexandre Favre, Dirk Theissen-Kunde, Luigi Bonacina, Sebastian Karpf, Pieter Vanden Berghe

Advances in High-Resolution Cryo Volume Electron Microscopy (cvEM) Imaging for Unicellular and Multicellular Organisms
M. Kobylynska, D. Nicholls, Z. Broad, J. Wells, A. Robinson, S. Marcotti, D. McGrouther, Q-L. Ch’ng, G.F. Esteban, N.D. Browning, R.A. Fleck

Open Blink: Low-cost TIRF microscopy for super-resolution imaging via µManager
Ran Huo, Jelle Komen, Moritz Engelhardt, Anaïs Millot, Jérôme Extermann, Kristin Grußmayer

Fluorescence anisotropy structured illumination microscopy for quantitative super-resolved mapping of cell microenvironment and cytoskeletal dynamics
Shu Gao, Wenyi Wang, Liang Qiao, Han Wang, Mingqiao Liu, Yiwei Hou, Guangwei Xin, Chunyan Shan, Donghyun Kim, Zhixing Chen, Meiqi Li, Peng Xi

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

Scanless temporal focusing enables high-speed three-dimensional quantitative phase microscopy
Yuechuan Lin, Xiang Zhang, Rebecca E Zubajlo, Zahid Yaqoob, Brian W. Anthony, Peter T. C. So

Enhanced 2D structured illumination microscopy: super-resolution with optical sectioning and reduced reconstruction artifacts
Sylvia Marie Steinecker, Henning Ortkrass, Jasmin Celine Schürstedt-Seher, Annika Kiel, Angela Kralemann-Köhler, Jan Schulte am Esch, Thomas Huser, Marcel Müller

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

Aberration-aware 3D localization microscopy via self-supervised neural-physics learning
Shuang Fu, Wei Shi, Eugene A. Katrukha, Xi Chen, Yue Fei, Ke Fang, Ruixiong Wang, Tianlun Zhang, Donghan Ma, Yiming Li

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

Tensile expansion microscopy applies mechanical force to super-resolve fixed and image live cellular samples
Vignesh Venkataramani, Danielle R. Latham, Ramita Arampongpun, Marouen Zammali, Tejasvin Shrikanth, Anshuman Mohapatra, Jason A. Guerrero, Roberto C. Andresen Eguiluz, Divita Mathur, Laura M. Sanchez, Lydia Kisley

A rapid, low-cost approach to solid immersion lens fabrication for enhanced resolution in optical microscopy
Liam M. Rooney, Jay Christopher, Shannan Foylan, Charlie Butterworth, Laura Copeland, Lewis D. Walker, Katie Coubrough, The SOMC 2025 Consortium, Gwyn W. Gould, Margaret R. Cunningham, Ralf Bauer, Gail McConnell

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

PSF-Driven Spatio-Temporal Blending in Fluorescence Lifetime Imaging Microscopy and Its Mitigation via Mean-Shift Super-Resolution-Based Masking
Mario González-Gutiérrez, Diana M. Vázquez-Enciso, Nicolás Mateos, Wonsang Hwang, Esley Torres-García, Haydee O. Hernández, Jenu V. Chacko, Iván Coto Hernández, Pablo Loza-Álvarez, Christopher Wood, Adan Guerrero

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

Physics-informed multi-encoder adaptive optics enables rapid aberration correction for intravital microscopy of deep complex tissue
Xiangzhang Cheng, Bo Wang, Li Luo, Zhaowei Sun, Sicong He

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

Nanoscale imaging of expanded cells and proteins with spontaneously blinking dyes
Danush Taban, Marvin Jungblut, Made Budiarta, Dominic A. Helmerich, Cerridwen Kiesel, Sarah E. Plutkis, Luke D. Lavis, Donatus Krah, Ali H. Shaib, Sören Doose, Philip Kollmannsberger, Silvio O. Rizzoli, Gerti Beliu, Markus Sauer

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

Constructing a single-objective oblique plane microscope (OPM) for fast, multi-colour, high-resolution volumetric fluorescence imaging
Ziwei Zhang, Wenzhi Hong, Yunzhao Wu, Arpan Dey, Andrew Shevchuk, David Klenerman

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

PAVR: High-Resolution Cellular Imaging via a Physics-Aware Volumetric Reconstruction Framework
Xuanwen Hua, Keyi Han, Zhi Ling, Olivia Reid, Zijun Gao, Hongmanlin Zhang, Edward A. Botchwey, Parvin Forghani, Wenhao Liu, Mithila Anil Sawant, Afsane Radmand, Hyejin Kim, James E Dahlman, Aparna Kesarwala, Chunhui Xu, Shu Jia

Pulsed-electron illumination does not reduce beam damage for imaging biological macromolecules
Vishal Kumar, Julika Radecke, K.V. Chinmaya, Inayathulla Mohammed, Ricardo C. Guerrero-Ferreira, Daniel Harder, Dimitrios Fotiadis, Henning Stahlberg

In-Chamber Sublimation: A Practical Approach for Mitigating Ice and Curtaining in Cryo-Electron Tomography Lamellae Preparation
Amy L. Bondy, Genís Valentín Gesé, Thomas Thersleff, B. Martin Hällberg

An Advanced Mobile Laboratory to enable field-based microbial ecology and cell biology across scales
N Leisch, S Baars, T Beavis, P Bertucci, C Bhickta, M Bonadonna, CM Brannon, L Burgués-Palau, P Cherek, F Chevalier, J Decelle, M Demulder, G Dey, O Dudin, E Duke, BD Engel, E Flaum, S Flori, B Gallet, P Guichard, A Halavatyi, V Hamel, M Jacobovitz, C Juery, M Laporte, S Mattei, F Mikus, K Mocaer, K Moog, M Olivetta, M Pavie, R Pepperkok, A Perez-Boerema, L Planat, M Prakash, EW Pyle, CR Rhodes, I Romero-Brey, P Ronchi, H Rosa, A Rubio Ramos, C Saint-Donat, Y Schwab, H Shah, AM Steyer, A Svetlove, G Toullec, F Vincent, T Wiegand, W Wietrzynski, D Yee, S Zwahlen

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

Back-illumination Phase Imaging Enables Nanoscale Drift Stabilization in Non-transparent Biological Tissues
Hanna Manko, Marc Tondusson, Adeline Boyreau, Morgane Meras, Stéphane Bancelin, Laurent Groc, Laurent Cognet

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

A biochemical probe for microtubule lattice integrity uncovers motor-caused lattice damage
Cornelia Egoldt, Luc Reymond, Joshua Tran, Aleksandar Salim, Marie-Claire Velluz, Sascha Hoogendoorn, Charlotte Aumeier

Absorption dipole effects on MINFLUX single molecule localization
Sjoerd Stallinga, Wenxiu Wang, Bernd Rieger

Characterizing MINFLUX imaging performance with DNA origami
Alexander H. Clowsley, Alexandre F. E. Bokhobza, Radoslav Janicek, Karol Kołątaj, Gabriela Bleuer, Lorenzo Di Michele, Guillermo P. Acuna, Christian Soeller

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

Computational aberration-corrected volumetric imaging of single retinal cells in the living eye
Guanping Feng, Dayn R Godinez, Zhongqiang Li, Stephanie Nolan, Hongkwan Cho, Elizabeth Kimball, Elia J. Duh, Thomas V Johnson, Ji Yi

Optical Windows for Transcranial Brain Imaging in Living Mice: Skull Thinning, Clearing, and Beyond
Yiming Fu, Gewei Yan, Zhentao She, Yingzhu He, Kangqi Liu, Jianan Qu

A pilot study for whole proteome tagging in C. elegans
Matthew Eroglu, Oliver Hobert