Microscopy preprints: bioimage analysis

Posted by FocalPlane, on 12 June 2026

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

Fluorescence Lifetime Imaging in Plants: Practical guidelines for multiplexing, label-free imaging and data analysis
Beatrice Lace Dr., Pascal Krohn Dr., Morgane Batzenschlager Dr., Vanessa Fiess, David Molina Dr., Laura Ragni Dr., Thomas Ott Prof.

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

VLab4Mic: prediction of structural resolvability in super-resolution microscopy
Damián Martínez, Bruno M. Saraiva, Tayla Shakespeare, Mark Bates, Dylan M. Owen, Christophe Leterrier, Mario Del Rosario, Ricardo Henriques

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

Vermeer: Autoregressive generative modeling of microscopy predicts protein localization
Sandeep Kambhampati, Eric Zimmermann, Emre Hayir, Kevin K. Yang, Fei Chen, Alex X. Lu

POPSICLE: Benchmark Datasets for Segmentation and Localization in CryoET
Jonathan Schwartz, Utz Heinrich Ermel, C. Braxton Owens, Zhuowen Zhao, Ariana Peck, Gus L.W. Hart, Grant J. Jensen, Bridget Carragher, Dari Kimanius

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

TomoScore: A Neural Network Approach for Quality Assessment of Cellular cryoET
Xuqian Tan, Xueting Zhou, Ethan Boniuk, Anisha Abraham, Zhili Yu, Valerie Dalton, Steven J. Ludtke, Zhao Wang

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

Easymode: general pretrained networks for cellular cryo-ET enable flexible approaches to subtomogram averaging
Mart G. F. So-Last, Alister Burt, Thomas Hale, Matteo Allegretti

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

Automated assembly of protein complexes from cryo-EM maps with structure-informed Monte Carlo Tree Search
Rohit Dilip, Songrong Jeff Qu, Zhen Chen, David Van Valen

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

TipQuant: A robust algorithm for quantitative analysis of spatiotemporally dynamic activities in tip-growing cells
Jingzhe Guo, Julian Le Gouic, Rémi Rosenthal, Ailing Zou, Xiang Zhou, Nicolas Brunel, Zhenbiao Yang, Xinping Cui

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

Celldetective: an AI-enhanced image analysis tool for unraveling dynamic cell interactions
Rémy Torro, Beatriz Díaz-Bello, Dalia El Arawi, Ksenija Dervanova, Lorna Ammer, Florian Dupuy, Patrick Chames, Kheya Sengupta, Laurent Limozin

A Decade of Deep Learning-based Biomedical Image Segmentation
Suhao Yu, Haojin Wang, Ningsen Wang, Sicheng Chen, Juncheng Wu, Zhenlong Yuan, Tianhao Qi, Zongwei Zhou, Fei Xia, Jun Ma, Yuyin Zhou

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

ATI_Box: A Simple tool for convolutional neural network-based image semantic segmentation
Tomasz Przygodzki

Supervised Deep Learning for Efficient Cryo-EM Image Alignment in Drug Discovery with cryoPARES
Ruben Sanchez-Garcia, Alex Berndt, Amir Apelbaum, Judith Reeks, Pamela A Williams, Carl Poelking, Charlotte M Deane, Michael Saur

TetraFuse: A Synergistic Four-Dimensional Dynamic Fusion Framework for Efficient and Robust Medical Image Classification
Yufei Gao, Jiaqi Li, Jing Xu, Qing Li, Ziyu Li, Guohua Zhao, Yucheng Shi, Xia Wu, Yameng Zhang

SortIT — A Tool For Assessing Observer Variability And Creating Ground Truth Image Classification Datasets
Wataru Uegami, Tom Bisson, Ethan N. Okoshi, Frederico Gaia Costa da Silva, Jijgee Munkhdelger, Kris Lami, Norman Zerbe, Andrey Bychkov, Junya Fukuoka

Quantifying the spatio-temporal image degradation under motion blur in fluorescence microscopy
Serafim Korovin, Kutay Ugurlu, Dylan Kalisvaart, Manon Kok, Rainer Heintzmann, Kirti Prakash, Carlas S. Smith

Mycol: A user-friendly app for automating analysis of microscopy images
Samuel Alan Bradley, Henry Webel, Giovanni Schiesaro, Marcel Skumantz, Olga Novillo-Sanjuan, Alexandra Panagou, Rafael Lucena-Marín, Emil D. Jensen, Antonio Di Pietro, Carlos G. Acevedo-Rocha

Blender tissue cartography: an intuitive tool for the analysis of dynamic 3D microscopy data
Nikolas Claussen, Cécile Regis, Susan Wopat, Matthew F. Lefebvre, Sebastian Streichan

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

Volumetric Denoising: An Approach to Boost Acquisition and Downstream Analysis of Volume Electron Microscopy
Bohao Chen, Fangfang Wang, Haoyu Wang, Yanchao Zhang, Zhuangzhuang Zhao, Haoran Chen, Hua Han, Xi Chen, Yunfeng Hua

3DBrainOne: an integrated end-to-end platform for 3D histological analysis of whole mouse brains
Daye Kim, Young-Gyun Park

Top Model Decision Tree: Selecting Segmentation Models for Reliable Quantitative Analysis in Low- and Ultralow-Dose CryoEM
Lynnicia N. Massenburg, Sita S. Madugula, Spenser R. Brown, Amber N. Bible, Chanda R. Harris, Lance X. Zhang, Kiara Parker, Scott T. Retterer, Jennifer L. Morrell-Falvey, Rama K. Vasudevan, Alexis N. Williams

Instant Prior-Free Resolution Enhancement for Cross-Modality Microscopy
Haohong Gan, Shiyi Peng, Hailian Hu, Xuan You, Yabo Guo, Ruiyang Guo, Ziliang Chen, Jun Qian

OptiCell3D: Precise inference of mechanical cell properties from microscopy imaging
Steve Runser, Kevin A Yamauchi, Marius Almanstötter, Franziska L Lampart, Federico Carrara, Lisa Conrad, Laura Schaumann, Roman Vetter, Dagmar Iber

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

BaSiCPy: Scalable and Robust Shading Correction for Optical Microscopy Images
Yu Liu, Yohsuke T. Fukai, Santiago Cano-Muniz, Victor Perez, Mihail Todorov, Germán Camargo Ortega, Timothy Morello, Alexander Jovanovic, Dirk Loeffler, Johannes C. Paetzold, Xun Xu, Phillipp Paulischka, Lorenz Lamm, Nan Ma, Ali Erturk, Timm Schroeder, Lucas Boeck, Denis Schapiro, Nicholas Schaub, Carsten Marr, Tingying Peng

Self-supervised Internal Learning Enhances Isotropic Resolution for Three-dimensional Fluorescence Microscopy
Mingzhe Wei, Pengcheng Xu, Junyu Liu, Xuesong Li, Xuhui Feng, Jun Zhu, Renwei Dong, Hengjia Ran, Wentao Zhu, Yubing Han, Yue Li, Min Guo, Huafeng Liu

CiliAI: Automated segmentation and compartment-specific fluorescence quantification of primary cilia in confocal microscopy images
Eliza Karapetian, Christoph Gerhardt, Emrah Nazif, Thorsten Pfirrmann

LFCT: A Benchmark Dataset for Low-Frame-Rate Cell Tracking in Long-Term Live-Cell Microscopy
Mina Gachloo, Tirthankar Biswas, Xiaoming Lu, Caroline M. Greene, Chandler K. Hargett, Katelyn R. Simancik, Marc R. Birtwistle, Federico Iuricich

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

Topology-aware reconstruction of cellular state landscapes from microscopy using self-supervised learning
Elisa Messori, Doaa Taha, Lisa Fournier, Anna Foix Romero, Virginie Uhlmann, Pascal Frossard, Cédric Vincent-Cuaz, Rickie Patani, Raphaëlle Luisier

SPIFEE — A pipeline for analyzing traces of live-cell fluorescence microscopy data
Colin Hogendorn, Ingrid R. Aragon, Samuel Dallon, Eric Batchelor

Universal approach to wave-optical calculations of point spread functions in microscopy (and beyond)
Ivan Gligonov, Lars Loetgering, Francisco Tenopala-Carmona, Chia-Lung Hsieh, Ingo Gregor, Jörg Enderlein

Automated Multimodal Correlative Registration for Organelle-Specific Molecular Imaging
Chixiang Lu, Kaiqiang Zhao, Di Cui, Gu Chen, Qian Yang, Hui Yang, Murong Zhao, Kaiyun Song, Mehran Nikan, Zhijie Li, Shanchao Zhao, Jinpeng Cen, Xincheng Qiu, Stephen G. Young, C. Frank Bennett, Punit Seth, Kai Chen, Xiaojuan Qi, Haibo Jiang

A general method for bootstrapping dense 3D segmentations from sparse 2D annotations
Vijay Venu Thiyagarajan, Arlo Sheridan, Kristen M. Harris, Uri Manor

Agentic-J: An AI Agent for Biological Microscopy Image Analysis
Lukas Johanns, Marilin Moor, Davide Panzeri, Yu Zhou, Xinyi Chen, Nora F. K. Pauly, Zixuan Pan, Matthias Gunzer, Andreas Müller, Yiyu Shi, Hedi Peterson, Jianxu Chen

MicroscopyMatching: Towards a Ready-to-use Framework for Microscopy Image Analysis in Diverse Conditions
Xiaofei Hui, Haoxuan Qu, Hossein Rahmani, Shuohong Wang, Jeff W. Lichtman, Jun Liu