Microscopy preprints – applications in biology

Posted by FocalPlane, on 31 October 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.

A whole-body cell type atlas mapped into an electron microscopy volume of an annelid worm
Adam Phillip Oel, Cyril Christophe Daniel Robert Cros, Leslie Pan, Elena Buglakova, Samuel Haury Parra, Luca Santangeli, Tobias Gerber, Nikolaos Papalopoulos, Hernando Martinez Vergara, David Puga, Vanessa Disela, Niederhaus Lara, Paola Yanina Bertucci, Victoria Witte, Asli Bilgesu Kilic, Idoia Quintana Urzainqui, Julieta Maria Acevedo, Jacob Musser, Anna Kreshuk, Detlev Arendt

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

Focused acoustic-radiation-force microscopy for live-cell selective nucleus deformation and nucleus viscoelasticity measurement
Natsumi Fujiwara, Hiroki Okita, Midori Uno, Kanta Adachi, Kichitaro Nakajima, Nobutomo Nakamura, Mee-Hae Kim, Masahiro Kino-oka, Kotaro Ogawa, Kensuke Ikenaka, Hirotsugu Ogi

Single-particle multi-parametric microscopy reveals structural, size, and payload heterogeneity in mRNA-loaded lipid nanoparticles
Albert Kamanzi, Ariadne Tuckmantel Bido, Yao Zhang, Erik Olsén, Maya Stibbards-Lyle, Martin Jasinski, Yifei Gu, Benjamin Wang, Michael Venier-Karzis, Romain Berti, Michelle Jeliazkova, Cynthia Shaheen, Jerry Leung, Miffy Hok Yan Cheng, Pieter Cullis, Sabrina Leslie

Excitation Spectral Phasor Microscopy (ExSPM) unveils spatiotemporal heterogeneities in polarity of intracellular lipid droplets
Jiayi Liu, Mingxuan Tang, Rui Yan, Jinhong Yan, Yi He, 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.

Combining FRET and super-resolution microscopy reveals kinase activation and mitochondrial activity at the nanoscale
Nicolas Y. Jolivet, Pierre-Jean Desmaison, Xavier Pinson, Olivier Delalande, Giulia Bertolin

Characterising cancer-stroma interactions through high-content phenotyping from microscopy time-lapses
Laura Wiggins, Jodie R. Malcolm, Karen Hogg, Peter J. O’Toole, Julie Wilson, William J. Brackenbury

Mapping EGFR1 sorting domains in endosomes with a calibrated 3D expansion microscopy toolkit
Tayla Shakespeare, Rajpinder S. Seehra, Neftali Flores Rodriguez, Nkolika Atuanya, Thomas M.D. Sheard, Ralf Köhler, Daniel Bose, Philip Woodman, Barbara Ciani, Izzy Jayasinghe

Cooperative Binding of Cytosolic Type III Secretion System Proteins to the Injectisome Revealed by Live-Cell Single-Molecule Localization Microscopy
Olivia Isabella Christiane de Cuba, Gopika Arumugam Lekshmi, Caroline Francis Tyndall, Andreas Gahlmann

Mechanism of beta-arrestin 1 mediated Src activation via Src SH3 domain revealed by cryo-electron microscopy
Natalia Pakharukova, Brittany N. Thomas, Harsh Bansia, Linus Li, Dana K. Bassford, Rinat R. Abzalimov, Jihee Kim, Alem W. Kahsai, Biswaranjan Pani, Kunhong Xiao, Roni Ochakovski, Shibo Liu, Xingdong Zhang, Seungkirl Ahn, Amedee des Georges, Robert J. Lefkowitz

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

Chromatin is a long-range force generator that regulates plasma membrane tension and cell integrity independently of gene expression
Aidan T. Cabral, Manasi Sawant, Minwoo Kang, Xie Liangqi, Hawa Racine Thiam

Offsetting ROS-mediated arrest of endothelial fenestration dynamics permits long-term optical super-resolution- and AFM-imaging
Annika Kiel, Marcin Luty, Angela Kralemann-Köhler, Laureen Patricia Helweg, Jasmin Schürstedt-Seher, Jerzy Kotlinowski, Jakub Pospíšil, Malgorzata Lekka, Thanh-Diep Ly, Thomas Huser, Jan Schulte am Esch, Wolfgang Hübner, Karolina Szafranska, Bartlomiej Zapotoczny

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

Fast Hyperspectral and Super-Resolved Mapping of Lipid Membrane Polarity with Single-Molecule Sensitivity
Elric Dion Pott, Meek Yang, James Ethan Batey, Joie Embree, Bin Dong

Stress-induced switch in small extracellular vesicle secretion: from constitutive ‘torn bag mechanism’ to exocytosis
Dorina Lenzinger, Lilla Lankovics, Istvan Dudas, Tunde Barkai, Zsofia Szasz, Krisztina V Vukman, Kelsey Fletcher, Attila Csomos, Zoltan Mucsi, Edina Bugyik, Csaba Cserep, Adam Denes, Szilvia Bosze, Edit I Buzas, Tamas Visnovitz

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

Nanoscopy of Organelle Handoff Portals Reveals Direct Coupling between ER Remodeling and Microtubule-Based Transport
Jin-Sung Park, Il-Buem Lee, Hyeon-Min Moon, Hyeonjun Jeon, MinHyeong Lee, Chungho Kim, Seok-Cheol Hong, Minhaeng Cho

Building without the architect: the dispensable role of MICOS in de novo cristae formation in malaria parasites
Silvia Tassan-Lugrezin, Irina Bregy, Judith López Orra, Nicholas I. Proellochs, Geert-Jan van Gemert, Rianne Stoter, Felix Evers, Taco W.A. Kooij, Laura van Niftrik

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

Spatial mapping of cell-surface protein glycosylation at molecular resolution
Dijo Moonnukandathil Joseph, Nathan Linus Sison, Nazlican Yurekli, Sheston Culpepper, Leonhard Möckl

Simultaneous Label-free Imaging of Nucleolar Dynamics and Subcellular Metabolic Shifts Across Tissue Contexts
Kunzan Liu, Ellen L. Kan, Honghao Cao, Jiashu Han, Giovanni de Nola, Linda G. Griffith, Eliezer Calo, Sixian You

Torque-generating units of the bacterial flagellar motor are rotary motors
Basarab G Hosu, Alina M Vrabioiu, Aravinthan D T Samuel

Label-free biochemical imaging and timepoint analysis of neural organoids via deep learning-enhanced Raman microspectroscopy
Dimitar Georgiev, Ruoxiao Xie, Daniel Reumann, Xiaoyu Zhao, Álvaro Fernández-Galiana, Mauricio Barahona, Molly M. Stevens

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

Synthetic pectin-cellulose nanofiber capsule provides minimal model capturing mechanics of a regenerating plant cell wall
Cyril Grandjean, Ravi Shanker, Sarah A. Pfaff, Anran Mao, Jordi Chan, Sophie Asnacios, Atef Asnacios, Sulin Zhang, Daniel J. Cosgrove, Enrico Coen, Anna J. Svagan, Pauline Durand-Smet

Leishmania amazonensis amastigotes invade non-phagocytic cells via highly localized parasite-induced actin remodeling
Thamires Queiroz-Oliveira, Laura Valéria Rios-Barros, Anna Luiza Silva-Moreira, Isadora Vieira Santos-Brasil, Julyanna Oliveira-Castro, Juliana Almeida, Marcos André Vannier-Santos, Jane Lima-Santos, Maria Fátima Horta, Thiago Castro-Gomes

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

Lipid transfer by ORP3 is required for the regulation of PI4P and PI(4,5)P2 at the plasma membrane in mitosis
Anaïs Vertueux, Agathe Verraes, Christie Ouaddi, Emilie Pellier, Véronique Proux-Gillardeaux, Laurence Walch, Mélina Heuzé, Cathy L. Jackson, Jean-Marc Verbavatz

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

Spatial Regulation of Lck Activation at the Immune Synapse Revealed by a FRET-Based Biosensor
Javier Casas

Spatio-temporal dynamics of macroglial cell organisation and proximity to blood vessels during postnatal development
Naomie Guille, Héloïse Monnet, Tristan Hourcade, Philippe Mailly, Martine Cohen-Salmon, Anne-Cécile Boulay

Label-free 3D subcellular phenotyping of mouse embryos by holotomography enables early prediction of blastocyst formation
Chungha Lee, Geon Kim, Taeseop Shin, Sangho Lee, Jae Young Kim, Kyoung Hee Choi, Jieun Do, Jaehyeong Park, Jaephil Do, Ji Hyang Kim, YongKeun Park

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

Cells dynamically adapt their nuclear volumes and proliferation rates during single to multicellular transitions
Vaibhav Mahajan, Keshav Gajendra Babu, Markus Mukenhirn, Antje Garside, Vinita Ajit Kini, Trishla Adhikari, Timon Beck, Byung Ho Lee, Carsten Werner, Alf Honigmann, Sebastian Aland, Raimund Schluessler, Anna Verena Taubenberger

The Rhizarian amoeba Filoreta ramosa develops a neuron-like arborized network using conserved cytoskeletal mechanisms
Sarah L. Guest, Scott C. Dawson

Removal of the Ciliary Gate Allows Axoneme Extension in the Absence of Retrograde IFT
Ana R. G. De-Castro, Maria J. G. De-Castro, Guus H. Haasnoot, Reto Gassmann, Erwin J. G. Peterman, Tiago J. Dantas, Carla M. C. Abreu

The Dynein-Dynactin complex influences amnioserosa cell morphodynamics and adhesion during Drosophila dorsal closure
Deepanshu Sharma, Maithreyi Narasimha

Cadherin Regulation of Endoplasmic Reticulum-Plasma Membrane Contact Sites
Sonam Lhamo, Navaneetha Krishnan Bharathan, William Giang, Kandice R. Levental, Cory L. Simpson, Stephanie Zimmer, Andrew P. Kowalczyk

Tubulin autoregulation factors SCAPER and TTC5 recruit γ-tubulin to non-centrosomal MTOCs for neuronal microtubule nucleation and axon regeneration
Yi Xie, Alessandro Comincini, Chengye Feng, Carrie Ann Davison, Marc Hammarlund, Francesca Bartolini, Shaul Yogev

3D multi-omic mapping of whole nondiseased human fallopian tubes at cellular resolution reveals a large incidence of ovarian cancer precursors
André Forjaz, Vasco Queiroga, Yajuan Li, Alfredo Hernandez, Ashleigh Crawford, Xiaoyu Qin, Mei Zhong, Margarita Tsapatsis, Saurabh Joshi, Donald Kramer, Oliver Nizet, Habin Bea, Yuhan Li, Shuo Qin, Robert O’Flynn, Mingder Yang, Brittany Pratt, Fan Wu, Paul Gensbigler, Max Blecher, Pei-Hsun Wu, Luciane T. Kagohara, Ie-Ming Shih, David Zwicker, Mark Atkinson, Lingyan Shi, Rong Fan, Ashley L. Kiemen, Denis Wirtz

The lipidomic architecture of the mouse brain
Luca Fusar Bassini, Halima Hannah Schede, Laura Capolupo, Leila Haj Abdullah Alieh, Francesca Venturi, Alessandro Valente, Colas Droin, Daniel Trejo Banos, Irina Khven, Ece Z. Asirim, Anita Nashrallah, Irmak Kaysudu, Ekaterina Krymova, Giovanni D’Angelo, Gioele La Manno

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

Endoplasmic Reticulum Geometry Dictates Neuronal Bursting via Calcium Store Refill Rates
Valentina Davi, Pierre Parutto, Cecile Crapart, Yuyi Zhang, Tasuku Konno, Joseph Chambers, John P Franklin, Daniel Maddison, Mosab Ali Awadelkareem, Michael J Devine, Elena Koslover, Edward Avezov

Mechanical coordination between anaphase A and B drives asymmetric chromosome segregation
Ana M. Dias Maia Henriques, Tim Davies, Serge Dmitrieff, Nicolas Minc, Julie C. Canman, Julien Dumont, Gilliane Maton

Structural insights into mitotic-centrosome assembly
Nada Mohamad, Siu-Shing Wong, Anupa Majumdar, Alan Wainman, Ingelise Holland-Kaye, Lars Hubatsch, Zsofia Novak, Andrey Pozniakovsky, Martine Ruer-Gruss, Andreas F.M. Haensele, Anna Caballe, Steven Johnson, Susan M. Lea, Anthony Hyman, Jordan W. Raff

Architecture and function of Bud3 and Bud4-induced septin structures
Ingrid E. Adriaans, Sandy Ibanes, Aurélie Bertin, Chantal Cazevieille, Joséphine Lai-Kee-Him, Marco Geymonat, Laura Picas, Simonetta Piatti

PAK4 promotes vertex remodeling to maintain epithelial integrity and barrier function
Babli Adhikary, Alexander Chang, Atsuko Y. Higashi, Hideki Chiba, Ann L. Miller, Tomohito Higashi

Diverse ancestral myosin motors generate and segregate distinct types of nanocluster-rich domains at the plasma membrane
Parijat Sil, Thomas S. van Zanten, Sowmya Jahnavi, Ajay Bansal, Suvrajit Saha, Bhagyashri Mahajan, Mukesh Kumar, Parvinder Pal Singh, Madan Rao, Satyajit Mayor

Spatial Expression Pattern and Cellular Organization of Gap Junctions in Third Instar Wing Imaginal Discs of Drosophila melanogaster
Spraha Bhandari, Ankita Chodankar, Franka Eckardt, Reinhard Bauer

Altering cell size asymmetry in Drosophila neural stem cells creates supernumerary stem cells with limited lineage expansion potential
Melissa K Delgado, J Ian Hertzler, Sophia Jannetty, Mia Hoover, Chang Yin, Ilara Yilmaz, Danielle Vahdat, Adam von Barnau Sythoff, Jay Z. Parrish, Neda Bagheri, Clemens Cabernard

Local RhoA activation induces septin recruitment
Shreya Chandrasekar, Margaret E. Utgaard, Bradley Somerfield, Huini Wu, Jordan R. Beach, Patrick W. Oakes

Multiscale imaging of cytokinesis
N. Hümpfer, Z. Marin, A. Zehtabian, K. Bruckmann, D. Spierling, J. Schmoranzer, J. Ries, H. Ewers

Super-resolution microscopy reveals a Rab6a-dependent trafficking hub for rhodopsin at the mammalian rod photoreceptor Golgi
Maryam Hekmatara, Samantha L. Thompson, Kristen N. Haggerty, Sydney Hagen, Brooke A. Brothers, Bali Daniels, Guillaume Luxardi, Ala Moshiri, Wen-Tao Deng, Michael A. Robichaux

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

A scalable long-term in vitro model of human colonic epithelium with continuous barrier function
Ashley J. Cuttitta, Sophia R. Meyer, Tristan Frum, Bhargavasai Gunuguntla, Angeline Wu, Sha Huang, Jack Morgan, Michael K. Dame, Jonathan Z. Sexton, Jason R. Spence

Piezo1–Yap1 signalling translates tissue mechanics into regenerative cell states
Fernando Ferreira, Jaime A. Espina, Artemis G. Korovesi, Inês A. Ferreira, Quentin Tirel, Elias H. Barriga

Adaptations in Plasmodium tubulin determine unique microtubule architectures, mechanics and drug susceptibility
Mamata Bangera, Jiangbo Wu, Daniel Beckett, Dominik Fachet, Josie L. Ferreira, Gregory A. Voth, Simone Reber, Carolyn A. Moores

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

The phosphoinositide PI5P impairs mitochondrial function through endosome-mitochondria proximity
Helene Tronchere, Sourour Ben Harzallah, Mathieu Cinato, Valentin Antoszewski, Vanessa Soldan, Stéphanie Balor, Oksana Kunduzova, Frank Lezoualc’h, Frederic Boal

Rnd3 regulates cell morphodynamics by spatial restriction of cell contraction signaling
Arya Sachan, Carolin Gierse, Suchet Nanda, Xiaoyi Xin, Yao-Wen Wu, Leif Dehmelt

Accessibility of the unstructured α-tubulin C-terminal tail is controlled by microtubule lattice conformation
Takashi Hotta, Morgan L. Pimm, Ezekiel C. Thomas, Yang Yue, Patrick DeLear, Lynne Blasius, Michael Cianfrocco, Morgan DeSantis, Ryota Horiuchi, Takumi Higaki, David Sept, Ryoma Ohi, Kristen J. Verhey

COPI-dependent intra-Golgi recycling at an intermediate stage of cisternal maturation
Adam H. Krahn, Areti Pantazopoulou, Jotham Austin II, Natalie Johnson, Conor F. Lee-Smith, Benjamin S. Glick

Mutating different α-tubulin acetylation sites has distinct effects on axon terminal morphogenesis in Drosophila melanogaster
Helen Than, Chloe J. Welch, Ethan Schauer, Sophia Truijillo, Jill Wildonger

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

Tissue surface mechanics constrains proliferation-driven forces to guide mammalian body axis elongation
Marc Trani-Bustos, Ryan G Savill, Arthur Boutillon, Petr Pospíšil, Deniz Conkar, Claudia Froeb, Johannes R Soltwedel, Heidi L van de Wouw, Ellen M Sletten, Jesse V Veenvliet, Otger Campàs

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

Self-organization of tumor heterogeneity and plasticity
Carlos Pérez-González, David B. Brückner, Mickael Di-Luoffo, Sophie Richon, Ruchi Goswami, Meryem Baghdadi, Florence Piastra-Facon, Neta Felsenthal, Réda Bouras, Arianna Fumagalli, Mirjam van der Net, Martijn Gloerich, Salvatore Girardo, Jochen Guck, Jacco van Rheenen, Julie Guillermet-Guibert, Edouard Hannezo, Danijela Matic Vignjevic

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

Fast calcium-dependent reorientation of motile cilia basal bodies in the simple metazoan, Trichoplax
Marvin Leria, Moina-mkou Daroueche, Magali Requin, Roman Hill, André Le Bivic, Raphaël Clément, Andrea Pasini

Combining brainwide activity imaging and electron microscopy reveals novel nociceptive circuits
Nadine Randel, Chen Wang, Michael S. Clayton, Kun Wang, Song Pang, Shan C. Xu, Andrew Champion, Harald F. Hess, Albert Cardona, Philipp J. Keller, Marta Zlatic

mTORC1 signaling modulate microtubule tyrosination/detyrosination status to regulate lysosome dynamics
Jeganath Ammavasai, Nitin Mohan

Contractile peri-nuclear actomyosin network repositions peripheral and polar chromosomes to promote early kinetochore–microtubule interactions
Nooshin Sheidaei, John K. Eykelenboom, Zuojun Yue, Graeme Ball, Alexander J.R. Booth, Tomoyuki U. Tanaka