Microscopy preprints – applications in biology

Posted by FocalPlane, on 16 May 2025

Here is a curated selection of preprints published recently. In this post, we share preprints that use microscopy tools to answer questions in biology.

Comprehensive 3D Imaging of Whole Zebrafish Using a Water-Based Clearing Reagent for Hard Tissues
Kiyohito Taimatsu, John Prevedel, Daniel Castranova, Kanako Inoue, Amit Puthan, Brant M. Weinstein

Figure extracted from Taimatsu, *et al.*

Single-cell dynamics reveal a stress-induced decision between cardiomyocyte hypertrophy and apoptosis
Bryan Chun, Lavie Ngo, Jeffrey J. Saucerman

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

Airway Secretory Cells Contain Both a Perinuclear Golgi Ribbon and Dispersed Golgi Satellites
Oanh N. Hoang, Colin E. Chan, Joshua M. Brenner, Denisse Leza-Rincon, Ana M. Jaramillo, Brendan Dolan, Adam W. Aziz, Rodolfo A. Cardenas, Gerardo J. Cardenas, Eduardo D. Galvez, Reid T. Powell, Leoncio Vergara, Harry Karmouty-Quintana, Jesper M. Magnusson, Gunnar C. Hansson, Roberto Adachi, John D. Dickinson, Christopher M. Evans, Justin A. Courson, Alan R. Burns, Michael J. Tuvim, Burton F. Dickey

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

Comprehensive Workflow for Imaging Live Insulin Secretion Events and Granules in Intact Islets
Margret A. Fye, Rahul Sharma, Phyu Sin M. Myat, Pi’ilani Regan, Hudson McKinney, Guoqiang Gu, Irina Kaverina

Curvature-dependent morphological reorganization of the endoplasmic reticulum determines the mode of epithelial migration
Simran Rawal, Pradeep Keshavanarayana, Diya Manoj, Purnati Khuntia, Sanak Banerjee, Basil Thurakkal, Rituraj Marwaha, Fabian Spill, Tamal Das

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

Unveiling the Molecular Architecture of T Cells and Immune Synapses with Cryo-Expansion Microscopy
Florent Lemaître, Olivier Mercey, Isabelle Mean, Elise Paulin, Valérie Dutoit, Jan Rath, Denis Migliorini, Caroline Arber, Paul Guichard, Virginie Hamel, Benita Wolf

Goblet cells mechanically breach the epithelial barrier in gut homeostasis
Justine Creff, Yuan He, Sandra Bernat-Fabre, Etienne Buscail, Salomé Neuvendel, Vishnu Krishnakumar, Thomas Mangeat, Shi-Lei Xue, Denis Krndija

Condensation of Sidekick at tricellular junctions organizes mechanical forces for cell-cell adhesion remodeling
Hiroyuki Uechi, Daxiao Sun, Yuki Saeki, Tetsuya Hiraiwa, Alf Honigmann, Anthony A. Hyman, Erina Kuranaga

The V-ATPase/ATG16L1 axis drives membrane remodeling during epithelial morphogenesis
Gabriel Baonza, Tatiana Alfonso-Pérez, Gonzalo Herranz, Carlos Quintana-Quintana, Carmen Gordillo-Vázquez, Yara El Mazjoub, L.M. Escudero, David G. Míguez, Elisa Martí, Nuria Martínez-Martín, Fernando Martín-Belmonte

Archaeal SegAB forms a bipolar structure that promotes chromosome segregation in spherical cells
Arthur Charles-Orszag, Samuel J Lord, Nadia Herrera, Luke Strauskulage, Arghya Bhowmick, Tom Goddard, Bianca Wassmer, Marleen van Wolferen, Garrison Asper, Amy Flis, Johnny Rodriguez, Sy Redding, Oren Rosenberg, Sonja-Verena Albers, R. Dyche Mullins

KIF5B and Dynein regulate adhesion-dependent Golgi organization and microtubule acetylation
Antara Chakraborty, Sharvari M. Pitke, BR Rajeshwari, Anwesha Dasgupta, Natasha Buwa, Rajalaxmi Behera, Madhavan Jayakrishnan, Nagaraj Balasubramanian

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

Lipid scrambling via TMEM16F mediates the formation and release of apoptotic vesicles
Trieu Le, Yu Meng Li, Amra Saric, Joost Holthuis, Sergio Grinstein, Spencer Freeman

Spindle-localized F-actin regulates polar MTOC organization and the fidelity of meiotic spindle formation
Edgar J. Soto-Moreno, Nourhan N. Ali, Florian Küller, Veselin Nasufovic, Michaela Frolikova, Olga Tepla, Jaromir Masata, Dirk Trauner, Amanda A. Patterson, Hans-Dieter Arndt, Katerina Komrskova, Magdalena Zernicka-Goetz, David M. Glover, Ahmed Z. Balboula

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

FRAP-in-SR: Fluorescence recovery in the Super-Resolution regime reveals subcompartments of 53BP1 foci
Chengchen Wu, Janeth Catalina Manjarrez-González, Muntaqa Choudhury, Noor Shamkhi, Siwen Ding, Vishnu M Nair, Viji M. Draviam

Phactr4 influences macrophage lamellipodial structure and dynamics through Arp2/3 complex and Ezrin regulation
Rohini Manickam, Jeremy D Rotty

The endoplasmic reticulum promotes microtubule organization and region-specific disassembly to execute Compartmentalized Cell Elimination
Karen Juanez, Hannah Selvarathinam, Madison Jones, Piya Ghose

Structure-Function Mapping of Olfactory Bulb Circuits with Synchrotron X-ray Nanotomography
Yuxin Zhang, Carles Bosch, Tobias Ackels, Alfred Laugros, Anne Bonnin, Jayde Livingstone, Carsten Waltenberg, Manuel Berning, Sina Tootoonian, Mihaly Kollo, Andrea Nathansen, Norman Rzepka, Peter Cloetens, Alexandra Pacureanu, Andreas T. Schaefer

Disruption of Plasma Membrane Lipid Asymmetry Alters Cellular Energetics
Pavel Barahtjan, Katelyn C. Cook, Václav Bočan, H. Mathilda Lennartz, Tobias Jumel, Kai Schuhmann, Sofia Traikov, Kristin Böhlig, Sascha M. Kuhn, Cristina Jiménez López, Tiago C. Alves, Andrej Shevchenko, Jonathan Rodenfels, André Nadler

Live-cell imaging reveals nutrient-dependent dynamics of ER-mitochondria contact formation via PDZD8
Saeko Aoyama-Ishiwatari, Koki Nakamura, Takahiro Nagao, Yusuke Hirabayashi

High resolution mapping of the actin fusion focus reveals myosin V-dependent transport of formin for actin aster compaction
Valentine Thomas, Hikari Mase, Laetitia Michon, Andrea Picco, Marko Kaksonen, Sophie G Martin

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

Unlocking new understanding of Plasmodium sporozoite biology with expansion microscopy
Benjamin Liffner, Thiago Luiz Alves e Silva, Elizabeth Glennon, Veronica Primavera, Elaine Hoffman, Alexis Kaushansky, Joel Vega-Rodriguez, Sabrina Absalon

Close-Up of vesicular ER Exit Sites by Volume Electron Imaging using FIB-SEM
Athul Nair, Akhil Nair, Patrick Stock, Arkash Jain, Elliott Somerville, Anwesha Sanyal, Tom Kirchhausen

Localizations and functions of septins are susceptible to epitope tagging
Jack R Gregory, Ian Mikale Llaneza, Aysha H Osmani, Haley E Gosselin, Jian-Qiu Wu

Talin1 adhesions’ morphology is largely unaffected by polyacrylamide substrate stiffness
Joanna Hajduk, Patrycja Twardawa, Zenon Rajfur, Zbigniew Baster

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

Single molecule imaging reveals extracellular signal-regulated kinases dependent signal responsive spatial regulation of translation in cardiomyocytes
Itai Erlich, Guy Douvdevany, Rami Haddad, Benjamin L. Prosser, Izhak Kehat

Deltaviruses spread through a viral Trojan Horse
Joe McKellar, Aurélien Fouillen, Sébastien Lyonnais, Florian Seigneuret, Marie-Pierre Blanchard, Antonio Trullo, Lorena Kumarasinghe, Sylvain De Rossi, Roni Sleiman, Solange Desagher, Raphael Gaudin, Hugues de Rocquigny, Sébastien Granier, Jussi Hepojoki, Karim Majzoub

Probing relaxed myosin states in hypertrophic cardiomyopathy by second harmonic-generation microscopy
Giulia Arecchi, Marica Dente, Weikang Ma, Beatrice Scellini, Nicoletta Piroddi, Marina Scardigli, Jingyuan Yu, Jing Zhao, Riccardo Cicchi, Ryo Kinegawa, Caroline Muellenbroich, Corrado Poggesi, Cecilia Ferrantini, Thomas Irving, Michael Regnier, Leonardo Sacconi, Chiara Tesi

Mechanism of bacterial outer membrane exchange revealed by quantitative microscopy
Elias J. Topo, Carolina Basurto De Santiago, Pengbo Cao, Daniel Wall, Beiyan Nan

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 Kumaran Nair, Sudarshan Gadadhar, Saravanan Palani

Excitation Spectral Phasor Microscopy (ExSPM) unveils spatiotemporal heterogeneities in polarity of intracellular lipid droplets
Jiayi Liu, Yi He, Rui Yan, Jinhong Yan, Ruirong Wang, Zhipeng Zhang, Jiankai Xia, Igor Kireev, Ke Xu, Kun Chen

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

High-content microscopy and machine learning characterize a cell morphology signature of NF1 genotype in Schwann cells
Jenna Tomkinson, Cameron Mattson, Michelle Mattson-Hoss, Herb Sarnoff, Stephanie J. Bouley, James A. Walker, Gregory P. Way

Mechanical forces drive mitochondrial matrix extrusion and apoptotic pore growth
Andreas Jenner, Timo Dellmann, Hyuntae Kim, David Gomez, Cristiana Zollo, Jürgen Köfinger, Katrin Seidel, Felix Gaedke, Astrid Schauss, Gerhard Hummer, Ana J. Garcia-Saez

Actin conformation dynamics precede force generation in cytotoxic T lymphocytes
Adam M Rochussen, Aybaran O Kebabci, Alexander K Winkel, Kristian Franze, Daniel A Fletcher, Gillian M Griffiths, Anna H Lippert

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

Outer epidermal edges mediate cell-cell adhesion for tissue integrity in plants
Özer Erguvan, Adrien Heymans, Asal Atakhani, Elsa Gascon, Richard S. Smith, Olivier Ali, Stéphane Verger

Nucleophagy is promoted by two autophagy receptors and inhibited by chromatin-nuclear envelope tethering in fission yeast
Zhu-Hui Ma, Zhao-Qian Pan, Zhao-Di Jiang, Guang-Can Shao, Yu Hua, Fang Suo, Chen-Xi Zou, Yi-Feng Jiang, Meng-Qiu Dong, Li-Lin Du

The architecture of membrane structures involved in hepatitis C virus genome replication revealed in close-to-native conditions by cryo-electron tomography
Upasana M. Sykora, Thomas J. O’ Sullivan, Yehuda Halfon, Juan Fontana, Mark Harris

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

Nucleus softens during herpesvirus infection
Aapo Tervonen, Simon Leclerc, Visa Ruokolainen, Katie Tieu, Sébastien Lyonnais, Henri Niskanen, Jian-Hua Chen, Alka Gupta, Minna U Kaikkonen, Carolyn A Larabell, Delphine Muriaux, Salla Mattola, Daniel E Conway, Teemu O Ihalainen, Vesa Aho, Maija Vihinen-Ranta

Mechanisms controlling the plasma membrane targeting and the nanodomain organization of the plant SPFH protein HIR2
Michal Daněk, Omar Hdedeh, Jessica Boutet, Héla Safi, Anas Abuzeineh, Amanda Martín-Barranco, Jean-Bernard Fiche, Caroline Mercier, Marcelo Nollmann, Yohann Boutté, Véronique Santoni, Sébastien Mongrand, Alexandre Martinière, Enric Zelazny

Pearling Drives Mitochondrial DNA Nucleoid Distribution
Juan C. Landoni, Matthew D. Lycas, Josefa Macuada, Willi Stepp, Roméo Jaccard, Christopher J. Obara, Andrew S. Moore, David Hoffman, Jennifer Lippincott-Schwartz, Wallace Marshall, Gabriel Sturm, Suliana Manley

Alpha-BET: Functional labeling of envelope glycoproteins with single domain antibodies for in-virus single molecule imaging
David J. Willliamson, Cecilia Zaza, Irene Carlon-Andres, Alessia Gentili, James L. Daly, Harry Holmes, Joseph W. Thrush, Tobias Starling, Stuart Neil, Ray Owens, Michael H. Malim, Christopher Tynan, Sabrina Simoncelli, Sergi Padilla-Parra

SlimVar: rapid in vivo single-molecule tracking of chromatin regulators in plants
Alex L. Payne-Dwyer, Geng-Jen Jang, Caroline Dean, Mark C. Leake

Measurements of Contractility in Actin Convergence Zone and KIF11-Inhibited Mitotic Spindles
Alexandre Matov, Andrea Bacconi