Microscopy preprints: applications in biology

Posted by FocalPlane, on 15 July 2026

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

Mechanical Tension Actively Triggers RhoA-Mediated Cell Extrusion
Fanny Wodrascka, Tianxiang Ma, Pablo Gottheil, Robin Durand, Lucas Anger, Andreas Schoenit, Mallica Pandya, Manon Arnaud, Tien Dang, Siavash Monfared, Guillaume Charras, René-Marc Mège, Amin Doostmohammadi, Benoit Ladoux, Simon de Beco

Hippocampal CA3 forms a two-layer network of molecularly distinct cell types in mice and humans
Rebecca J Morse-Mora, Yoav Ben-Simon, Satish Arcot Jayaram, Karl Rössler, Peter Jonas, Jake F Watson

The IFT-A complex plays a major role in the assembly of anterograde intraflagellar transport trains
Adeline Mallet, Thierry Blisnick, Eloïse Bertiaux, Cécile Fort, Manuel Majrouh, Sylvain Trépout, Philippe Bastin

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

Size-dependent nucleus-vacuole interactions in budding yeast demonstrate a role for steric packing in organelle shape and positioning
Mary Mirvis, Oghosa H. Akenuwa, Irene Tan, Christopher T. Lee, Wallace F. Marshall

Investigating nanostructure and -mechanics of contracting actin stress fibers by scanning ion conductance microscopy
Yanjun Zhang, Yasufumi Takahashi, You-Rong Lin, Andrew Shevchuk, Yuri Korchev, Clemens M. Franz

An adhesion GPCR regulates cell adhesion and mating in the closest living relatives of metazoans
Alain Garcia De Las Bayonas, Stefany Gonzalez, Nicole King

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

Actin cross-linking organizes basal body patterning through anomalous diffusion transitions
Raghavan Thiagarajan, Younes Farhangi Barooji, Poul-Martin Bendix, Mandar M. Inamdar, Jakub Sedzinski

4D spatial transcriptomics reveals nodule identity emerges through stacked parallel developmental programs
Min-Yao Jhu, Jo Heffer, Chongjing Xia, Thiago Alexandre Moraes, Claire M. Mulvey, Dario Bressan, Chen Liu, Jin-Peng Gao, Philip Poole, Katharina Schiessl, Giles E. D. Oldroyd

Cryogenic volume electron microscopy of whole plant protoplasts
Xiao Zhang, Zihan Lin, Xinlin Chen, Jake Kaminsky, Liguo Wang, Qun Liu

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

Nanoscale visualization of ribonucleoprotein condensates with ultrastructure RNA expansion microscopy
Jeet Mukhopadhyay, Parakbritta Hazra Dutta, Samiran Bhowmik, Pintu Patra, Mainak Bose

Monitoring Sphingomyelin Biosynthesis at Nanoscale Resolution by Expansion Microscopy
Fabienne Wagner, Arpita Mohanty, Fabian Schumacher, Julian Fink, Louise Kersting, Burkhard Kleuser, Jürgen Seibel, Vera Kozjak-Pavlovic, Thomas Rudel, Marcel Rühling

Deep learning-based decoding of axonal ultrastructure in gene-edited mice using electron microscopy imaging
Nianqi Deng, Guillaume Miao, Hooman Bagheri, Alan C Peterson, Anmar Khadra

Microscopy-informed structural connectivity mapping in the in vivo human brain via domain adaptation
Silei Zhu, Nicola K. Dinsdale, Saad Jbabdi, Karla L. Miller, Amy F.D. Howard

Using digital holographic microscopy (DHM) to monitor effects of extracellular matrix (ECM) glycation on cancer cell morphology and migration
Anupom Dep Nath, Estelle Leclerc, Stefan W Vetter

Super-resolution expansion microscopy reveals nanoscale protein domains and CO2-dependent remodeling of Chlamydomonas pyrenoid-traversing membranes
Aastha Garde, Haoyu Wu, Martin Jonikas

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

Multiscale three-dimensional ultrastructural mapping of intestinal tissues and organoids
Thijs Makaske, Vincent Hellebrekers, Albert K. Serweta, Dimitrios Laskaris, Saskia J.E. Suijkerbuijk, Sabine A. Fuchs, Kerstin Schneeberger-Verjaal, Jacco van Rheenen, Ihor Smal, Lukas C. Kapitein

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

High-resolution volumetric intravital imaging reveals asymmetric serotonin-dependent post-shock activity in the Drosophila brain
Heng Chang, Yueh-Feng Wu, Ching-Che Charng, Kai-Chun Jhan, Shun-Chi Wu, Ann-Shyn Chiang, Hsiao-Chun Amy Lin, Chung-Chuan Lo, Bi-Chang Chen, Sung-Jan Lin, Li-An Chu

Coordinated membrane remodeling and fission-fusion drive mitochondrial patterning during development
H Aravind, Vivek Kumar, Vaishali Modha, Manish Jaiswal

Ultrastructural diversity and subcellular organization of nigral Lewy pathology in Parkinson’s disease
Amanda J Lewis, Lukas van den Heuvel, Marta di Fabrizio, Kaliya Bandelier, Daria Proniakova, Domenic Burger, Notash Shafiei, Kazadi Ekundayo, Selene Offringa, Evelien Huisman, John GJM Bol, Wilma DJ Van de Berg, Henning Stahlberg

Direct visualization of Na,K-ATPase clustering by 3D DNA-PAINT MINFLUX nanoscopy
Bruno Stojcic, Ana Agostinho, Luca Panconi, Hans Blom, Hjalmar Brismar

Cryoelectron tomography of HIV-1 cell-cell transmission conjugates reveals a secluded environment for viral assembly and transfer
Jacob Jensen, Marcela Cunha, Broti Adhikary, Zaida Rodriguez, Iszavier Moe, Jasmine Beldin, Dmitry Lyumkis, Luiza Mendonça

Mechanical forces stimulate Golgi export
Chandini Bhaskar Naidu, Javier Vera Lillo, Eugenia Almacellas, Anabel-Lise Le Roux, Sabine Bardin, Nicolas Mateos, Jessica Angulo-Capel, Adam Wolowczyk, Yugo Terashima, Yuichi Wakana, Pere Roca-Cusachs, Maria F. Garcia-Parajo, Franck Perez, Bruno Goud, Jean-Baptiste Manneville, Stéphanie Miserey, Felix Campelo

Cell Mechanics Regulate Membrane Tubulation-Driven Trogocytosis in Adherent Cells
Tanishka Agrawal, Binayak Banerjee, Shubham Padhi, Kishal Roy, Neha Paddillaya, Adhisha Roy, Santanu Talukder, Namrata Gundiah, Shivprasad Patil, Saroj K. Nandi, Sunando Datta

Spatio-temporal Force Patterns Reveal a Mechanical Set Point in Early T Cell Activation
Farah Mustapha, Martine Biarnes-Pelicot, Jana El Husseiny, Remy Torro, Kheya Sengupta, Pierre-Henri Puech

Mitochondrial morphology and function are tuned by microtubule association
Nida Ul Fatima, Gregory MI Redpath, Zeenat Jahan, Olivia Nassar, Nicholas Ariotti, Vaishnavi Ananthanarayanan

Differential spatial regulation and activation of integrin nanoclusters inside focal adhesions
Sarah Keary, Amaris Guevara-Garcia, Nicolas Mateos, Felix Campelo, Maria F. Garcia-Parajo

Distinct nanoscale organizations of mucins and trans-sialidases in Trypanosoma cruzi
Gonzalo Escalante, Raquel Parada-Puig, Lucía F. Lopez, Alan M. Szalai, María de los Milagros Cámara, Luciano A. Masullo, Oscar Campetella, Juan Mucci, Fernando D. Stefani

Structure of the mammalian ciliary transition zone microtubule doublet
Bin Cai, Aitor Pellicer Carmadiel, Emma J. van Grinsven, Timo van Veghel, Amol Aher, Ellen Aarts, Yixin Xu, Pedro Beltro, Jeffrey M. Beekman, Anna Akhmanova, Jingwei Xu, Michal Wieczorek

Unbranched SPIN90-Arp2/3 actin promotes stress fiber speed and focal adhesion maturation
Luther W. Pollard, Andrew J. Steen, Qing Tang

ATAD3A structurally links mtDNA replication and mitochondrial fission
Nitish Dua, Boyuan Ma, Samantha Oviedo, Hamidreza Rahmani, Tumara Boyd, Donghyun Park, R. Luke Wiseman, Danielle A. Grotjahn

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

Tunneling nanotubes mediate mitochondrial homeostasis in cancer
Ines Saenz-de-Santa-Maria, Anna Pepe, Christel Brou, Jean-Yves Tinevez, Iakov Vitrenko, Thomas Cokelaer, Elizabeth Cohen-Jonathan Moyal, Roberto Weigert, Chiara Zurzolo

Machine learning-assisted Repli-Histo labeling reveals distinct transcription-dependent constraints on chromatin motion in living cells
Katsuhiko Minami, Kako Nakazato, Sachiko Tamura, S. S. Ashwin, Kazuhiro Maeshima

Dynein-microtubule forces drive nucleokinesis and transmigration in T cells
Yerbol Tagay, Alexander S. Zhovmer, Nandini Sarkar, Jorik Stoop, Linjun Su, Laurel Fleszar, Eric Peterman, Jeffrey P. Rasmussen, Alexander X. Cartagena-Rivera, Denis Tsygankov, Erdem D. Tabdanov

RBMP2 shapes specialized membranes for CO₂ delivery in the pyrenoid condensate
Haoyu Wu, Aastha Garde, Philippe Van der Stappen, Shan He, Jessica H. Hennacy, Shixin Yang, Zhiheng Yu, Benjamin D. Engel, Martin C. Jonikas

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

Early immune cell development precedes gastrulation in annual killifish
Sydney M. Sattler, Nicholas C. Lammers, Sebastian V. Hriscu, Clare L.T. Booth, Cole Trapnell, Philip B. Abitua

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

Ionic Exposure History Shapes Inner Nuclear Membrane Voltage and Chromatin Texture Responses
Hamid Sediqi, Juanita Mathews, Giovanni de Nola, Abigail K. R. Lytton-Jean, Michael Levin

Compositionally unique mitochondria in filopodia support cellular migration
Madeleine Marlar-Pavey, Daniel Tapias-Gomez, Marcel Mettlen, Jonathan R. Friedman

Connectivity Logic of Dendritic Spines in Cortex: Increased Inputs and Ensemble Formation
Dean Geckt, Netanel Ofer, Michael W. Reimann, Rafael Yuste, Idan Segev

A multimodal perturbation atlas defines the phenotypic resolution of cellular morphology
Chad Liu, Alexander Hillsley, Madhurya Sekhar, Cassidy A. Jones, Gabriel Sturm, Taihei Fujimori, Diane M. Wiener, Karen W. Cheng, Talon Chandler, Duo Peng, Leah C. Dorman, Ilakkiyan Jeyakumar, Max Frank, Alex Lin, Ivan E. Ivanov, Greg Courville, Chris B. Charlton, Eduardo Hirata-Miyasaki, Sydney Ripsky, Lin Luan, Ziwen Liu, Trang Le, Yiyun Rao, Giovanni Palla, Vincent Turon-Lagot, Miguel Cid-Rosas, Carolina Arias, Norma F. Neff, Alan R. Lowe, Shalin B. Mehta, Loïc A. Royer, Rafael Gómez-Sjöberg, Manuel D. Leonetti

Harmala alkaloids regulate cell division planes in plants
Kamryn A. Diehl, Shayyaine Ocampo-Dallas, Olivia S. Hazelwood, Joh Demura-Devore, Fabiola Muro-Villanueva, Ryan S Nett, M. Arif Ashraf