Microscopy preprints – bioimage analysis

Posted by FocalPlane, on 3 October 2025

Here is a curated selection of preprints published recently. In this post, we focus specifically on bioimage analysis and data management.

scPortrait integrates single-cell images into multimodal modeling
Sophia C. Mädler, Niklas A. Schmacke, Alessandro Palma, Altana Namsaraeva, Ali Oğuz Can, Varvara Varlamova, Lukas Heumos, Mahima Arunkumar, Georg Wallmann, Veit Hornung, Fabian J. Theis, Matthias Mann

VASCilia (Vision Analysis StereoCilia): A Napari Plugin for Deep Learning-Based 3D Analysis of Cochlear Hair Cell Stereocilia Bundles – update
Yasmin M. Kassim, David B. Rosenberg, Samprita Das, Zhuoling Huang, Samia Rahman, Ibraheem Al Shammaa, Samer Salim, Kevin Huang, Alma Renero, Cayla Miller, Yuzuru Ninoyu, Rick A. Friedman, Artur Indzhykulian, Uri Manor

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

FAST: Filamentous Actin Segmentation Tool for quantifying cytoskeletal organization
Vineeth Aljapur, Adam Gardner, Jason Carayanniotis, Andrew R. Harris

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

CenSegNet: a generalist high-throughput deep learning framework for centrosome phenotyping at spatial and single-cell resolution in heterogeneous tissues
Jiaoqi Cheng, Keqiang Fan, Miles Bailey, Xin Du, Rajesh Jena, Costantinos Savva, Mengyang Gou, Ramsey Cutress, Stephen Beers, Xiaohao Cai, Salah Elias

ShapeEmbed: a self-supervised learning framework for 2D contour quantification
Anna Foix Romero, Craig Russell, Alexander Krull, Virginie Uhlmann

MuSpAn: A Toolbox for Multiscale Spatial Analysis – update
Joshua A. Bull, Joshua W. Moore, Shania M. Corry, Muyang Lin, Hayley L. Belnoue-Davis, Eoghan J. Mulholland-Illingworth, Simon J. Leedham, Helen M. Byrne

nERdy: network analysis of endoplasmic reticulum dynamics – update
Ashwin Samudre, Guang Gao, Ben Cardoen, Bharat Joshi, Ivan Robert Nabi, Ghassan Hamarneh

TopoTome: Topology-informed unsupervised segmentation and analysis of 3D images
Samuel Bourgeat, Fani Derveni, Victoire Gamblin, Ece Naz Bilgiç, Feyza Nur Arslan, Andrew Oates, Can Aztekin, Fides Zenk, Pedro M. Reis, Ana Marija Jakšić

FishFeats: streamlined quantification of multimodal labeling at the single-cell level in 3D tissues
Gaëlle Letort, Tanya Foley, Ilona Mignerey, Laure Bally-Cuif, Nicolas Dray

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

Depositing biological segmentation datasets FAIRly – update
Elaine ML Ho, Dimitrios Ladakis, Mark Basham, Michele C Darrow

MorphoNet 2.0: An innovative approach for qualitative assessment and segmentation curation of large-scale 3D time-lapse imaging datasets – update
Benjamin Gallean, Tao Laurent, Kilian Biasuz, Ange Clement, Noura Faraj, Patrick Lemaire, Emmanuel Faure

DINOSim: Zero-Shot Object Detection and Semantic Segmentation on Microscopy Images – update
Aitor González-Marfil, Estibaliz Gómez-de-Mariscal, Ignacio Arganda-Carreras

Deep Learning-Based Segmentation of 2D Projection-Derived Overlapping Prospore Membrane in Yeast – update
Shodai Taguchi, Keita Chagi, Hiroki Kawai, Kenji Irie, Yasuyuki Suda

SXTractor: A Self-Supervised Feature Extractor of Soft X-Ray Images That Enables Few-Shot Tomogram Segmentation
ShaoSen Chueh, Madeleen C. Brink, Jeremy C. Simpson, Sergey Kapishnikov

Vertically Integrated System for Tracking and Assessing cell-cycle aware phenotypes under confinement
Melissa Pezzotti, Eloisa Torchia, Julius Zimmermann, Sara Rigolli, Alessandro Enrico, Moises Di Sante, Francesco S. Pasqualini

Automated Image-Based Profiling of Pluripotent Stem Cell Colonies
Rui Geng, Benjamin L. Kidder

Mapping human microglial morphological diversity via handcrafted and deep learning-derived image features
Kayhan Alvandipour, Amélie Weiss, Mona Mathews, Brenda Besemer, Michaela Segschneider, Zahra Hanifehlou, Michael Peitz, Arnaud Ogier, Peter Sommer, Oliver Brüstle, Johannes H. Wilbertz

Segmentation-guided photon pooling enables robust single cell analysis and fast fluorescence lifetime imaging microscopy
Kayvan Samimi, Danielle E Desa, Xiaotian Zhang, Dan L Pham, Rupsa Datta, Melissa C Skala

Uni-AIMS: AI-Powered Microscopy Image Analysis
Yanhui Hong, Nan Wang, Zhiyi Xia, Haoyi Tao, Xi Fang, Yiming Li, Jiankun Wang, Peng Jin, Xiaochen Cai, Shengyu Li, Ziqi Chen, Zezhong Zhang, Guolin Ke, Linfeng Zhang