Microscopy preprints – new tools and techniques in imaging

Posted by FocalPlane, on 28 November 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!

Customizable FDM-based zebrafish embryo mold for live imaging
Marcela Xiomara Rivera Pineda, Jaakko Lehtimäki, Guillaume Jacquemet

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

A toolkit for testing membrane-localising tags across species
Irene Karapidaki, Mette Handberg-Thorsager, Tsuyoshi Momose, Hitoyoshi Yasuo, Grigory Genikhovich, Sarah Assaf, Clara Deleau, Ying Pang, Clayton Pavlich, Beke Lohmann, Maria Lorenza Rusciano, Mattia Stranges, Juliette Mathieu, Marie Zilliox, Kirill Ustyantsev, Bastien Salmon, Béryl Laplace-Builhé, Manon Koenig, Jeffrey J. Colgren, Maria Ina Arnone, Eugene Berezikov, Thibaut Brunet, Gregor Bucher, Pawel Burkhardt, Daniel J. Dickinson, Evelyn Houliston, Jan Huisken, Lucas Leclère, Michalis Averof

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

Multiplexed embryo profiling links cellular state to zygotic genome activation in single cells
Max Hess, Marvin F. Wyss, Edlyn Wu, Joel Lüthi, Chiara Rebagliati, Nadine L. Vastenhouw, Darren Gilmour, Shayan Shamipour, Lucas Pelkmans

Chemogenetic modulation of luciferase emission color for imaging and sensing
Horgan Manirakiza, Yuriy Shpinov, Amandine Gontier, Lina El Hajji, Ludovic Jullien, Arnaud Gautier

Prodan-based solvatochromic probes for polarity imaging of organelles
Nathan Aknine, Paula Holban, Franziska Ragaller, Pablo Carravilla, Cenk O. Gurdap, Agit Cetinkaya, Erdinc Sezgin, Andrey S. Klymchenko

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

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.

napariTFM: An Open-Source Tool for Traction Force Microscopy and Monolayer Stress Microscopy
Artur Ruppel, Dennis Wörthmüller, Martial Balland, François Fagotto

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

Pulsed laser lensing for phase modulation in electron microscopy
Daniel X. Du, Adam C. Bartnik, Cameron J. R. Duncan, Usama Choudhry, Tanya Tabachnik, Chaim Sallah, Yuki Ogawa, Ebrahim Najafi, Ding-Shyue Yang, Jared M. Maxson, Anthony W. P. Fitzpatrick

Dual-Channel Event Microscopy for Ultrafast Biological Imaging
Ruipeng Guo, Xueli Pan, Qilin Deng, Abrar Ahmed, Qianwan Yang, Joseph Greene, Tongyu Li, Suet Ying Chan, Zhixiong Chen, Guorong Hu, Hui Feng, Lei Tian

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

Polarization MultiFocus Microscopy for volumetric super-resolution and orientation imaging of biofilaments
Louise Régnier, Caio Vaz Rimoli, Simli Dey, Feng-Ching Tsai, Guillermo A. Orsi, Sophie Brasselet, Bassam Hajj

Effects of biological fixation methods on stimulated Raman scattering microscopy signal
Chiara Ceconello, Wuji Han, Bryce Manifold, Dario Polli, Aaron Streets

Hybrid Solid-Liquid Optics Enable Scalable, High-Resolution, Multi-Immersion Light-Sheet Microscopy
Cheng Gong, Pauline Affatato, Matt Fay, Sudha R. Guttikonda, Nathan J. O’Connor, Emerson Noble, Maci Heal, Benjamin Haydock, Renee Mapa, Estanislao Daniel De La Cruz, Johanna E. Kowalko, Maria Antonietta Tosches, Charles R. Gerfen, Rene Hen, Christopher D. Makinson, Hanina Hibshoosh, Jack Glaser, Raju Tomer

Open Raman Microscopy (ORM): A Modular Hardware and Software Framework for Accessible Raman Imaging
Kevin T. Uning, Henry Brisebois, Conor C. Horgan, Magnus Jensen, Yue Yuan, Shiyue Liu, Elzbieta Stepula, Steven Vanuytsel, Vishal Kumar, Stephen Goldrick, Robert D. Knight, Martin A. B. Hedegaard, Michael B. Albro, Mads S. Bergholt, Michael R. Thomas

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

High-Resolution Imaging of the Rhizosphere Using Resin-Embedded Cross-Sectional Polishing and Scanning Electron Microscopy for Biological Samples (bioCP-SEM)
Kiminori Toyooka, Yuko Saito, Yumi Goto, Mayuko Sato

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 F. Hess

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

Mid-Infrared Photothermal Mesoscopy with Millimeter Field of View and Sub-micron Spatial Resolution
Rong Tang, Jiaze Yin, Bethany Weinberg, Haonan Lin, Jiahui Lu, David Gate, Oxana Klementieva, Ji-Xin Cheng

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

Mechanical de-skewing enables high-resolution imaging of thin tissue slices with a mesoSPIM light-sheet microscope
Steven Moreno, Sharika Mohanan, Ahmed Elnageh, Erin Boland, Lewis Williamson, Camilla Olianti, Leonardo Sacconi, Godfrey Smith, Eline Huethorst, Caroline Müllenbroich

Altair-LSFM A High-Resolution, Easy-to-Build Light-Sheet Microscope for Sub-Cellular Imaging
John Haug, Seweryn Gałecki, Hsin-Yu Lin, Xiaoding Wang, Kevin M. Dean

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

Acridine Orange dye for long-term staining and live imaging of cnidarian development and regeneration
Vaidehi Patel, Valeria Dountcheva, Labib Rouhana

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

Correlative 4D-STEM Ptychography and EELS for Cryogenic Single-Particle Analysis
Xiaopeng Wu, Yu Lei, Peng Wang

Microsecond Time-Resolved Cryo-EM Based on Jet Vitrification
Michal Haubner, Harry M. Williams, Jakub Hruby, Monique S. Straub, Albert Guskov, Kirill Kovalev, Marcel Drabbels, Ulrich J. Lorenz

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

BRET-Based Mitochondrial Subcompartment Localization Biosensors
Abdulrasheed O. Abdulrahman, Mathias Lescuyer, Rami El Zein, Erika Cecon, Julie Dam, Bernard Masri, Ralf Jockers

Quantitative comparison of methodologies for translation site imaging in living cells
Agata D. Misiaszek, Esther Griesbach, Egle Jaugaite, Aurelio Ortale, Jan Eglinger, Tobias Hochstoeger, Jeffrey A. Chao

STED-FCS in subdiffraction limit volumes reveals altered diffusion in live cell applications
Bernd Zobiak, Maria Andres-Alonso, Yuanyuan Wang, Behnam Mohammadi, Christian Gorzelanny, Hermann Clemens Altmeppen, Shuting Yin, Antonio Virgilio Failla

Protocol for the Synthesis of Green Fluorescence Carbon Quantum Dots and Biological Application
Himanshu Khatri, Ankesh Kumar, Raghu Solanki, Pankaj Yadav, Dhiraj Bhatia, Amit K. Yadav

In Vivo Calcium Imaging in the Near-Infrared II Window
Danyang Xu, Zhisheng Wu, Hui Yang, Gu Chen, Wayne Jason Li, Xingyu Yue, Guang-Lei Wang, Sixin Xu, Hanze Yu, Yuanhua Liu, Zideng Dai, Haibo Jiang, Long-jiang Yu, Hongjie Dai, Feifei Wang

A software-based focus system for wide-field optical microscopy
Ilyas Djafer-Cherif, Bartlomiej Waclaw

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

Super-resolution microscopy via fluctuation-enhanced spatial mode demultiplexing
Stanislaw Kurdzialek

Pulsed heterodyne Brillouin microscopy enables high-specificity, low-phototoxicity biomechanical imaging with single-ended access
Zi-Xuan Du, Shuai Yao, Yun Qi, Jin-Rui Zhang, Jun-Lin You, Zhisheng Yang, Ting Mi, Jingjing Xie, Wei-Biao Chen, Long Zhang, Fan Yang

Depth-enhanced molecular imaging with two-photon oblique plane microscopy
Kevin Keomanee-Dizon, Yaakov Clenman, Alejandra Duran, Sergey Ryabichko, Pauline Hansen, Tohn Borjigin, Richard Thornton, Jared E. Toettcher, Harold M. McNamara