Microscopy preprints – bioimage analysis

Posted by FocalPlane, on 11 July 2025

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

Enabling Real-Time Fluctuation-Based Super Resolution Imaging
Jelle Komen, Miyase Tekpınar, Ran Huo, Klarinda de Zwaan, Nergis Tomen, Kristin Grußmayer

SMART: An Integrated Platform Revolutionizing Cryo-Electron Microscopy Workflow from Data Acquisition to Atomic Modeling
Haibin Liu, Yangyu Wu, Wenpeng Zhang, Huaican Xu, Zhenqian Guo, Fanhao Meng, Xinyu Men, Allen Chunlong Guo

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

Plug-and-Play automated behavioral tracking of zebrafish larvae with DeepLabCut and SLEAP: pre-trained networks and datasets of annotated poses
Leandro A. Scholz, Tessa Mancienne, Sarah J. Stednitz, Ethan K. Scott, Conrad C.Y. Lee

SAMJ: Fast Image Annotation on ImageJ/Fiji via Segment Anything Model
Carlos Garcia-Lopez-de-Haro, Caterina Fuster-Barcelo, Curtis T. Rueden, Jonathan Heras, Vladimir Ulman, Daniel Franco-Barranco, Adrian Ines, Kevin W. Eliceiri, Jean-Christophe Olivo-Marin, Jean-Yves Tinevez, Daniel Sage, Arrate Munoz-Barrutia

Corelative light and electron microscopy (CLEM) image registration by blood vessel axes alignment
Y. Van den Berghe, A. Kremer, D. Verhaege, R.E. Vandenbroucke, Y. Saeys

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

CALIPERS: Cell cycle-aware live imaging for phenotyping experiments and regeneration studies
Moises Di Sante, Melissa Pezzotti, Julius Zimmermann, Alessandro Enrico, Joran Deschamps, Elisa Balmas, Silvia Becca, Samantha Solito, Alessandro Reali, Alessandro Bertero, Florian Jug, Francesco S. Pasqualini

DynaCLR: Contrastive Learning of Cellular Dynamics with Temporal Regularization
Eduardo Hirata-Miyasaki, Soorya Pradeep, Ziwen Liu, Alishba Imran, Taylla Milena Theodoro, Ivan E. Ivanov, Sudip Khadka, See-Chi Lee, Michelle Grunberg, Hunter Woosley, Madhura Bhave, Carolina Arias, Shalin B. Mehta

Deep Learning Pipeline for Segmentation and Quantification of Overlapping Membranes in 2D Image
Shodai Taguchi, Keita Chagi, Hiroki Kawai, Kenji Irie, Yasuyuki Suda

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

Explainable Artificial Intelligence in Biomedical Image Analysis: A Comprehensive Survey
Getamesay Haile Dagnaw, Yanming Zhu, Muhammad Hassan Maqsood, Wencheng Yang, Xingshuai Dong, Xuefei Yin, Alan Wee-Chung Liew

Graphical and Interactive Spatial Proteomics Image Analysis Workflow
Pritpal Singh, Jocelyn H. Wright, Kimberly S. Smythe, Bryce Fukuda, Ling-Hong Hung, Cecilia CS Yeung, Ka Yee Yeung

LazySlide: accessible and interoperable whole slide image analysis
Yimin Zheng, Ernesto Abila, Eva Chrenková, Juliane Winkler, André F. Rendeiro

PathoEye: a deep learning framework for the whole-slide image analysis of skin tissue
Yusen Lin, Feiyan Lin, Yongjun Zhang, Jiayu Wen, Guomin Li, Xinquan Zeng, Hang Sun, Hang Jiang, Teng Yan, Ruzheng Xue, Hao Sun, Bin Yang, Jiajian Zhou

Unpaired Image-to-Image Translation for Segmentation and Signal Unmixing
Nikola Andrejic, Milica Spasic, Igor Mihajlovic, Petra Milosavljevic, Djordje Pavlovic, Filip Milisavljevic, Uros Milivojevic, Danilo Delibasic, Ivana Mikic, Sinisa Todorovic

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

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

A Statistical Framework for Robust and Reproducible BioImage Analysis
David J. Barry, Stefania Marcotti, Lina Gerontogianni, Gavin Kelly

AlliGator: Open Source Fluorescence Lifetime Imaging Analysis in G
X. Michalet

A quantitative pipeline for whole-mount deep imaging and analysis of multi-layered organoids across scales
Alice Gros, Jules Vanaret, Valentin Dunsing-Eichenauer, Agathe Rostan, Philippe Roudot, Pierre-Francois Lenne, Leo Guignard, Sham Tlili

Software for semi-automatic analysis of microscopic images of adhesion structures and protein colocalization in cells
Joanna Hajduk, Patrycja Twardawa, Zenon Rajfur

Uncertainty-aware quantitative analysis of high-throughput live cell migration data
Simo Kitanovski, Shannon Conroy, Justin Sonneck, Madeleine Dorsch, Sebastian Urban, Jianxu Chen, Barbara M. Grüner, Daniel Hoffmann