Microscopy preprints – new tools and techniques in imaging

Posted by FocalPlane, on 13 June 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!

IntAct-U-ExM: Ultrastructure Expansion microscopy of actin networks via an internally-tagged actin
Anubhav Dhar, Nishaant Kumar Palani Balaji, Sanjana Mullick, Sucheta Dey, Angana Ghosh, Deepak Nair, Sudarshan Gadadhar, Saravanan Palani

Silicon nitride PIC beam formers for light sheet fluorescent microscopy
Alireza Tabatabaei Mashayekh, Jeremy Witzens

Cleared tissue dual-view oblique plane microscopy
Liuba Dvinskikh, Hugh Sparks, Darren Ennis, Raffaele Sarnataro, David Carreno, David T. Riglar, Paula Cunnea, Iain A. McNeish, Chris Dunsby

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

3D Gaussian Adaptive Reconstruction for Fourier Light-Field Microscopy
Chenyu Xu, Zhouyu Jin, Chengkang Shen, Hao Zhu, Zhan Ma, Bo Xiong, You Zhou, Xun Cao, Ning Gu

Fifth Harmonic and Five-Photon Excitation Fluorescence Multiphoton Microscopy
Joshua H. Magnus, Lam T. Nguyen, Elana G. Alevy, Travis W. Sawyer, Samuel D. Crossley, Khanh Kieu

SmartEM: machine-learning guided electron microscopy
Yaron Meirovitch, Ishaan Singh Chandok, Core Francisco Park, Pavel Potocek, Lu Mi, Shashata Sawmya, Yicong Li, Thomas L. Athey, Vladislav Susoy, Neha Karlupia, Yuelong Wu, Daniel R. Berger, Richard Schalek, Caitlyn A. Bishop, Daniel Xenes, Hannah Martinez, Jordan Matelsky, Brock A. Wester, Hanspeter Pfister, Remco Schoenmakers, Maurice Peemen, Jeff W. Lichtman, Aravinthan D.T. Samuel, Nir Shavit

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

MagnEspScope – DIY microscope with integrated magnetic system for magnetogenetic studies
A.S. Minin, M.A. Uimin, A.V. Belousova, I.V. Zubarev

Reconceptualizing Smart Microscopy: From Data Collection to Knowledge Creation by Multi-Agent Integration
P.S. Kesavan, Pontus Nordenfelt

Reflected Inline Detection in Epi Oblique Plane Microscopy
Md Nasful Huda Prince, Balasubramanian Chellammal Muthubharathi, Wishwa Herath, Nikhil Sain, Md Rafiqul Islam Rupam, Aadil Qadir Bhat, Adil R. Wani, Mubarak Hussain Syed, Tae-Hyung Kim, Mark C. Walker, Olga Ponomarova, Tonmoy Chakraborty

Dc-EEMF: Pushing depth-of-field limit of photoacoustic microscopy via decision-level constrained learning
Wangting Zhou, Jiangshan He, Tong Cai, Lin Wang, Zhen Yuan, Xunbin Wei, Xueli Chen

Deep Volumetric Localization Super-Resolution Microscopy
Keyi Han, Xuanwen Hua, Tianrui Qi, Zijun Gao, Xiaopeng Wang, Shu Jia

Two-photon microscopy through scattering media harnessing speckle autocorrelation
Lei Zhu, Bernhard Rauer, Hilton B. De Aguiar, Sylvain Gigan

Ultra-wide-field, deep, adaptive two-photon microscopy
Mengke Yang, Zhen-Qiao Zhou, Song Lang, Hanqing Zheng, Shuai Chen, Tong Li, Eline Stas, Long Zhang, Zhi Zhang, Volkan Uzungil, Qinying Liu, Yu Huang, Lyu Jing, Yimei Li, Hongbo Jia, Min Li, Xiaojing Li, Jingwei Li, Yuguo Tan, Gong Yan, Simon R Schultz

Cryogenic light microscopy of vitrified samples with Ångstrom precision
Hisham Mazal, Franz-Ferdinand Wieser, Daniel Bollschweiler, Vahid Sandoghdar

Optimizing effective labeling efficiency in MINFLUX 3D DNA-PAINT microscopy by maximizing marker detection probability
Christian Soeller, Alexandre F. E. Bokhobza, Javier Casares-Arias, Alexander H. Clowsley

Chromatix: a differentiable, GPU-accelerated wave-optics library
Diptodip Deb, Gert-Jan Both, Eric Bezzam, Amit Kohli, Siqi Yang, Amey Chaware, Cédric Allier, Changjia Cai, Geneva Anderberg, M. Hossein Eybposh, Magdalena C. Schneider, Rainer Heintzmann, Fabrizio A. Rivera-Sanchez, Corey Simmerer, Guanghan Meng, Jovan Tormes-Vaquerano, SeungYun Han, Sibi Chakravarthy Shanmugavel, Teja Maruvada, Xi Yang, Yewon Kim, Benedict Diederich, Chulmin Joo, Laura Waller, Nicholas J. Durr, Nicolas C. Pégard, Patrick J. La Rivière, Roarke Horstmeyer, Shwetadwip Chowdhury, Srinivas C. Turaga

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

Two-Dimensional Nonlinear Structured Illumination Microscopy with rsEGFP2
Shaoheng Li, Ryo Tamura, Kota Banzai, Daichi Kamiyama, Peter Kner

3D X-ray microscopy lights up nanoparticles in plants
Emil V. Kristensen, Francesca Siracusa, Andrea Pinna, Idil Ertem, Augusta Szameitat, Julie Villanova, Xiaoyu Gao, Adrian Schiefler, Dominique J. Tobler, Subhasis Ghoshal, Søren Husted, Rajmund Mokso

A flexible framework for automated STED super-resolution microscopy
David Hörl

In vivo deep-brain microscopy at submicrometer resolution with refractive index-matched prism interfaces
Taiga Takahashi, Yuanyuan Zhou, Motosuke Tsutsumi, Chihiro Ito, Azumi Hatakeyama, Hirokazu Ishii, Akiyoshi Saitoh, Hiroshi Yukawa, Junichi Nabekura, Tomomi Nemoto, Kohei Otomo, Naoji Matsuhisa, Masakazu Agetsuma

Cryo-Correlative Light and X-ray microscopies: Expanding the Intracellular Chemical Map
D. Karpov, L. Cuau, R. Shishkov, C. Gramaccioni, E. Dallerba, B.J. Schwehr, M. J. Hackett, S. Plush, M. Massi, F. Lerouge, P. Cloetens, S. Bohic

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

Multi-spectral optoacoustic microscopy driven by gas-filled hollow-core fiber laser pulses
Cuiling Zhang, Marcello Meneghetti, J. E. Antonio-Lopez, Rodrigo Amezcua-Correa, Yazhou Wang, Christos Markos

Cell Morphology and Biophysical Mechanisms-Informed Traction Force Microscopy Using Machine Learning
Koki Fujiwara, Ryosuke Fujikawa, Yukihiro Suzuki, Kenta T. Suzuki, Yuichi Sakumura

Oblique Thick Light-Sheet Microscopy with Spatiotemporal 3D Localization for RNA Imaging in Intact 50 μm-Thick Sections
Lin Cai, Qihang Song, Dongjian Cao, Qihuan Li, Wanchen Wu, Yinghao Xiao, Xingguang Chen, Shujing Huang, Jie Yang, Yingjun Zhang, Zhen-Li Huang

A workflow integrating organ-on-chip culture and correlative 3D light and electron microscopy for microtissue analysis
Judith M. Schaart, Dorothee Wasserberg, Marcos A. Eufrásio Cruz, Mariska Kea-te Lindert, Robin H.M. van der Meijden, Rona Roverts, Nataliya Debera, Minh Phu Lu, Jeroen Rouwkema, Wouter H. Nijhuis, Andries D. van der Meer, Pascal Jonkheijm, Nico Sommerdijk, Anat Akiva

Volumetric single-molecule tracking inside subcellular structures
Sam Daly, Joseph E. Chambers, Caroline Jones, Bin Fu, James D. Manton, Joseph S. Beckwith, Stefan J. Marciniak, David C. Gershlick, Steven F. Lee

A Spectral Image Scanning Microscope for Multi-Color High-Resolution Imaging
Lanna Bram, Ofir Tal-Friedman, Neta Fibeesh, Yohai Bar-Sinai, Eli Flaxer, Yael Roichman, Uri Ashery, Yuval Ebenstein, Jonathan Jeffet

Subcellular mass spectrometry imaging of lipids and nucleotides using transmission geometry ambient laser desorption and plasma ionisation
Reuben S.E. Young, Ann-Katrin Piper, Luke McAlary, Jayden C. McKinnon, Jeremy S. Lum, Jens Soltwisch, Marcel Niehaus, Shane R. Ellis

Ultrathin Liquid Cells for Microsecond Time-Resolved Cryo-EM
Wyatt A. Curtis, Jakub Hruby, Constantin R. Krüger, Sarah V. Barrass, Marcel Drabbels, Ulrich J. Lorenz

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

Mid-infrared chemical imaging of living cells enabled by plasmonic metasurfaces
Steven H. Huang, Po-Ting Shen, Aditya Mahalanabish, Giovanni Sartorello, Jenny Li, Xuefeng Liu, Gennady Shvets

Chip-Based 3D Interferometric Nanoscopy
Wei Wang, Hangfeng Li, Yilin Wang, Samuel F. H. Barnett, Zengxin Huang, Pakorn Kanchanawong

Super-resolution imaging in whole cells and tissues via DNA-PAINT on a spinning disk confocal with optical photon reassignment
Cecilia Zaza, Megan D. Joseph, Olivia P. L. Dalby, Rhian F. Walther, Karol Kołątaj, Germán Chiarelli, Franck Pichaud, Guillermo P. Acuna, Sabrina Simoncelli

High-fidelity generalizable light-field reconstruction of biological dynamics with physics-informed meta neural representation
Chengqiang Yi, Jiahao Sun, Minglu Sun, Lanxin Zhu, Yifan Ma, Sicen Wu, Yuting Liu, Shangbang Gao, Meng Zhang, Yuhui Zhang, Zhaoqiang Wang, Hsiai K. Tzung, Peng Zou, Binbing Liu, Dongyu Li, Peng Fei

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

Wide-field fluorescence lifetime imaging of single molecules with a gated single-photon camera
Nathan Ronceray, Salim Bennani, Marianna Fanouria Mitsioni, Nicole Siegel, Maria J. Marcaida, Claudio Bruschini, Edoardo Charbon, Rahul Roy, Matteo Dal Peraro, Guillermo P. Acuna, Aleksandra Radenovic

Cryo-EM Sample Preparation with Soft-Landing and Laser Flash Melting
Sarah V. Barrass, Tim K. Esser, Nathan J. Mowry, Lukas Eriksson, Jakub Hruby, Laurence T. Seeley, Wyatt A. Curtis, Lindsay A. Baker, Marcel Drabbels, Stephan Rauschenbach, Ulrich J. Lorenz

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

A Set of Novel Far-Red Fluorescent Proteins for Temporal Domain Multiplexing and Super-Resolution Imaging
Fakorede Olumayowa, Zhien Rong, Ruizhao Wang, Stavrini Papadaki, Xinyue Wang, Jiayue Cao, Fedor V. Subach, Reinhard W. Köster, Kazuhiko Namikawa, Kiryl D. Piatkevich

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

High-Speed Multiplexed DNA-PAINT Imaging of Nuclear Organization Using an Expanded Sequence Repertoire
Abhinav Banerjee, Micky Anand, Mansi Srivastava, Vedanth Shree Vidwath, Mahipal Ganji

Deep three-photon functional imaging in the mouse cortex with adaptive optics
Huriye Atilgan, Jingyu Wang, Qi Hu, Sandra Tan, Blake Russell, Martin J. Booth, Armin Lak

A parallelly distributed microscope and software system for scalable high-throughput multispectral 3D imaging
Hehai Jiang, Logan A Walker, Ye Li, Bin Duan, Xiaoman Niu, Jung-Chien Hsieh, Peng Yin, Mou-Chi Cheng, Hanquan Su, Kuanwei Sheng, Jessica P. Tang, Kenneth Athukorala, Stacey Greene, Ruby Pan, Arya Parlapalli, Meng Cui, Dawen Cai

Implantable CMOS Deep-Brain Fluorescence Imager with Single-Neuron Resolution
Sinan Yilmaz, Jaebin Choi, Ilke Uguz, Jongwoon Kim, Alejandro Akrouh, Adriaan J. Taal, Victoria Andino-Pavlovsky, Heyu Yin, Jason D. Fabbri, Laurent Moreaux, Michael L. Roukes, Kenneth L. Shepard

Bright and Photostable Voltage Sensors Derived from mBaoJin
Hanbin Zhang, Shihao Zhou, Tatiana P. Kuzmicheva, Oksana M. Subach, Christiane Grimm, Minho Eom, Shulamit Baror-Sebban, Yoav Adam, Young-Gyu Yoon, Valentina Emilliani, Fedor V. Subach, Kiryl D. Piatkevich

A large 3D-printed integrated lens-biprism element enhances contrast in transmission stereomicroscopy
Liam M. Rooney, William B. Amos, Shannan Foylan, Jay Christopher, Charlie Butterworth, Ralf Bauer, Gwyn W. Gould, Gail McConnell

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

CoVET: Cryo-Electron Tomography guided by optical electrophysiology
Mingyu Jung, Gwanho Ko, Dongsung Lim, Seonghoon Kim, Sojeong Kim, Young-Joon Kim, Myunghwan Choi, Soung-Hun Roh

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

VS-FPM: large-format, label-free virtual histopathology microscopy
Christopher Bendkowski, Adam P. Levine, Manuel Rodriguez-Justo, Laurence B. Lovat, Marco Novelli, Michael Shaw

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