Microscopy preprints: bioimage analysis

Posted by FocalPlane, on 4 September 2026

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

FOCUS-3D: Robust, generalizable volumetric cell segmentation for three-dimensional fluorescence microscopy
Qinghua Zhang, Zeyu Mu, Boqi Liu, Yunfeng Chi, Donglin Li, Wenjuan Wang, Jian-Quan Ni, Yinan Wan, Li Yu, Joaquín Navajas Acedo, Guoqiang Yu

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

NuclearIDTracker resolves intestinal cell identity and lineage dynamics through nuclear phenotypic signatures
Nguyen T.B. Nguyen, Rutger N.U. Kok, Sira Gevers, Xuan Zheng, Max A. Betjes, Lukas Ritter, Danny Feijtel, Matthew B. Smith, Sam F.B. van Beuningen, Jeroen S. van Zon, Sander J. Tans, María J. Rodríguez Colman

Trustworthy in silico labeling via semantic visual interpretability of image-to-image translation
Lion Ben Nedava, Gad Miller, Nitsan Elmalam, Matheus P. Viana, Jianxu Chen, Nathalie Gaudreault, Susanne M. Rafelski, Assaf Zaritsky

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

Cell Cycle Phases, Spindle Dynamics and Kinesin-5 Motor Localization Characterized by Deep Learning, Dual Segmentation and Decision-Tree Pipeline
Omer Bushusha, Karin Zarnitsky, Neta Yanir, Mayan Sadan, Daniel Sevilla Sánchez, Larisa Gheber

ImpRes: A robust FRAP framework to quantify fast diffusion of cytoplasmic probes
Olivier Destrian, René-Marc Mège, Benoît Goyeau, Morgan Chabanon

Probing intracellular physical environments by rotational and translational single-particle tracking
Dimitri Schumacher, Martin D. Baaske, Wenxin Zhang, Biswajit Pradhan, Delong Li, Thorsten Feichtner, Florian Wilfling, Eugene Kim

BactoMate: an integrated platform for reproducible bacterial microscopy analysis
Lasse Hallenga, Sarah Fornoff, Matthias Pesch, Dietrich Kohlheyer, Shazeb Ahmad, Jens Hör, Marc Erhardt, Philipp F. Popp

QuantEM: An optimized platform of vision transformer-based models for segmentation and analysis of electron microscopy data
Christopher Acree, Evan Krystofiak, Kathryn Coate, Kathleen DelGiorno, Nathan Winn, Sammy Weiser Novak, Elma Zaganjor, Mark Magnuson, Rafael Arrojo e Drigo

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

CryoLigATE: enhancing the resolvability of cryo-EM maps in protein-ligand complexes using deep learning
Nandan Haloi, Rebecca J. Howard, Erik Lindahl

Discrete Inverse Rendering: Biological Image Analysis with Integer Programming
Frans Zdyb, Julius B. Kirkegaard

Figure extracted from Zdyb and Kirkegaard. The image is made available under a CC-BY 4.0 International license.

ZenReg: A modular Python platform for fast and memory-efficient N-dimensional microscopy image registration
Fabrizio Musacchio, Martin Fuhrmann

OMIO: A policy-driven Python library for reproducible microscopy image I/O
Fabrizio Musacchio, Henrike Antony, Arush Baijal, Sophie Crux, Falko Fuhrmann, Nala Gockel, Denise Marie Hoffmann, Dilek Mercan, Felix Christopher Nebeling, Katharina Wolff, Martin Fuhrmann

From Generation to Discrimination: Vision Foundation Models for Synthetic SEM Image Detection
A. Palangattu, A. K. Sah, S. Raman, K. Pushpavanam

ACCREDIT: A Quality-Aware Agentic Engine for Cell-resolved Cross-modal Image Registration with Dynamic Iterative Tuning
Le Zhou, Faming Zhao, Tao Ren, Shaun M. Goodyear, Chengyun Tang, Baiyi Li, Tingting Zhang, Yabing Chen, Rosalie C. Sears, Gordon B. Mills, Adel Kardosh, Zheng Xia

Multi-channel high-density single-molecule localization
Hao Sha, Lucas-Raphael Müller, Nestor Miguel Castillo Duque de Estrada, Maxime Mathieu, Arthur Jaques, Zach Marin, Yongbing Zhang, Jakob H. Macke, Jonas Ries

GIAnT: a Glutamate Imaging Analysis Toolbox
Michael E. Xie, Johannes Friedrich, Elizabeth Wirsching, Caleb Jones Shibu, Maedeh Seyedolmohadesin, Naveen Ouellette, Tim Wang, Karel Svoboda, Adam S. Charles, Kaspar Podgorski

Celldega: Integrated Toolkit for Visualization and Analysis of Spatial Data
Nicolas Fernandez, Jaspreet Ishar, Huan Wang, Amin Ben Saad, Michal Lipinski, Samouil L. Farhi

Kiosc: an integrated platform for managing bioinformatics data analysis containers
Federico Marotta, Oliver Stolpe, Benedikt Obermayer, January Weiner, Manuel Holtgrewe, Dieter Beule, Mikko Nieminen

SynthMLM: A framework for interpretable analysis and synthetic localisation data generation for SMLM
Louis Gall, Sandeep Shirgill, Helen Abbott, Daniel J. Nieves, Dylan M. Owen