Microscopy preprints: bioimage analysis

Posted by FocalPlane, on 29 December 2025

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

CochleaNet: deep learning-based image analysis for cochlear connectomics and gene therapy
Lennart Roos, Aleyna Miraç Diniz, Elisabeth Koert, Martin Schilling, Mara Uhl, Anupriya Thirumalai, Mostafa Aakhte, Kathrin Kusch, Jan Huisken, Tobias Moser, Constantin Pape

micromorph: a Python toolkit for measurement of microbial morphology
Simone Coppola, Séamus Holden

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

Fast Loading and Transformation of Large-Volume Bioimaging Data Consistently Approaching the I/O Peak Speed Lin Cai, Xuzhong Qu, Hang Zhou, Ning Li, Xianyu Gou, Shiwei Li, Jian Huang, Shasha Guo, Xiuli Liu, Xiaohua Lv, Tingwei Quan, Shaoqun Zeng

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

A semi-automated pipeline for morphological analysis of myonuclei along single muscle fibers
Esben T. Schroeder, Helia G. Megowan, Madeline Luu, Adam Shuaib, Adam C. Fries, Jake Searcy, Hans C. Dreyer

Quantitative Network Classification with CLaSSiNet Reveals Nanoscale Organizational Principles of the Membrane Skeleton
Yuan Tao, Ruobo Zhou

IsoNet2 determines cellular structures at submolecular resolution without averaging
Yun-Tao Liu, Hongcheng Fan, Jonathan Jih, Liam Tran, Xiaoying Zhang, Z. Hong Zhou

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

Classifying Calcium Imaging Dynamics with Deep Learning: Multi-Frequency Analysis through Quantile-Based Time-Series Network Representations
Caroline L. Alves, Simone Hufgard, Margot Mayer, Helena Dasch, Andriana S. L. O. Campanharo, Loriz Francisco Sallum, Francisco A. Rodrigues, Christiane Thielemann

SIRP: A Self-Supervised Fluorescence Denoising method with Implicit Representation Priors
Yuze Li, Jun Zhu, Pengcheng Xu, Min Guo, Yue Li, Huafeng Liu

Dataset creation for supervised deep learning-based analysis of microscopic images — review of important considerations and recommendations
Christof A. Bertram, Viktoria Weiss, Jonas Ammeling, F. Maria Schabel, Taryn A. Donovan, Frauke Wilm, Christian Marzahl, Katharina Breininger, Marc Aubreville

Rewards-based image analysis in microscopy
Kamyar Barakati, Yu Liu, Utkarsh Pratiush, Boris N. Slautin, Sergei V. Kalinin

EMCF ecosystem: Towards pretrained foundation model for electron microscopy image analysis
Zeyu Yu, Jiansheng Guo, Feng Liu, Mengze Du, Shan Xu, Guowei Zhang, Li Xie, Bo Han, Zhonghua Chen, Gaoliang Deng, Chen Rui, Yong He, Xuping Feng

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

IDR searcher: a search engine solution for public image resource
Khaled Mohamed, William Moore, Dominik Lindner, Josh Moore, Jason R. Swedlow, Petr Walczysko, Frances Wong, Jean-Marie Burel

Image-guided alignment of consecutive multi-modal tissue slides
Benedetta Manzato, Claudio Novella Rausell, Gangqi Wang, Nina Ogrinc, Rosalie G.J. Rietjens, Marleen E. Jacobs, Christos Botos, Sebastien J. Dumas, Ton J. Rabelink, Ahmed Mahfouz

MAGNET: an all-in-one foundation model for cross-modal and cross-dimensional microscopic image restoration
Yifan Ma, Tianfeng Zhou, Lanxin Zhu, Chengqiang Yi, Yunshi Zhou, Binbing Liu, Peng Fei

Classpose: foundation model-driven whole slide image-scale cell phenotyping in H&E
Soham Mandal, José Guilherme de Almeida, Nickolas Papanikolaou, Trevor A Graham

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

An Accessible Python Framework for Real-Time Magnetic Tweezers Microscope Control and Image Processing
James A. London, Abhishek K. Singh, Teague C. Svendsen, Naciye Esma Tirtom, Zachary A. Root, Richard Fishel

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

Leveraging CryoEM and AI-Driven Morphological Feature Analysis for Insights on Bacterial Structures
Sita Sirisha Madugula, Lynnicia N. Massenburg, 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

LivecellX: Corrective Deep Learning for Object-Oriented Single-Cell Analysis in Live-Cell Imaging
Ke Ni, Gaohan Yu, Zhiqian Zheng, Yong Lu, Sophia Hu, Dante Poe, Sijie Zhang, Mia Sanborn, Mostofa Uddin, Zilin Wang, Shiman Zhou, Yanshuo Chen, Xueying Zhan, Weikang Wang, Jianhua Xing

Robust Deep Learning-based 3D Segmentation and Morphological Analysis of Mitochondria using Soft X-ray Tomography
Arun Yadav, Anshu Singh, Aneesh Deshmukh, Pushkar Bharadwaj, Anuj Baliyan, Kate White, Jitin Singla

TransiScope: An Interactive Open-Source Platform for Automated Detection and Analysis of Transient Events in Time-Lapse Microscopy
Rinki Dasgupta, Kaushik Das

CryoSiam: self-supervised representation learning for automated analysis of cryo-electron tomograms
Frosina Stojanovska, Ricardo M. Sanchez, Rasmus K. Jensen, Julia Mahamid, Anna Kreshuk, Judith B. Zaugg

Micro𝕊plit: Semantic Unmixing of Fluorescent Microscopy Data
Ashesh Ashesh, Federico Carrara, Igor Zubarev, Vera Galinova, Melisande Croft, Melissa Pezzotti, Daozheng Gong, Francesca Casagrande, Elisa Colombo, Stefania Giussani, Elena Restelli, Eugenia Cammarota, Juan Manuel Battagliotti, Nikolai Klena, Moises Di Sante, Raghabendra Adhikari, Daniel Feliciano, Gaia Pigino, Elena Taverna, Oliver Harschnitz, Nicola Maghelli, Norbert Scherer, Damian Edward Dalle Nogare, Joran Deschamps, Francesco Pasqualini, Florian Jug

Mastodon: the Command Center for Large-Scale Lineage-Tracing Microscopy Datasets
Johannes Girstmair, Tobias Pietzsch, Vladimir Ulman, Stefan Hahmann, Matthias Arzt, Mette Handberg-Thorsager, Samuel Pantze, Ko Sugawara, Robert Haase, Jean-Yves Tinevez, Pavel Tomancak

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

Chart Builder: An Interactive Tool for User Driven Data Visualization in the Electron Microscopy Data Bank
Neli Fonseca, Amudha Kumari Duraisamy, Zhe Wang, Sriram Somasundharam, Minoosadat Tayebinia, Lucas C. de Oliveira, Miao Ma, Jack Turner, Ardan Patwardhan, Gerard J. Kleywegt, Matthew Hartley, Kyle L. Morris

Towards improved particle averaging for single-molecule localization microscopy using geometric deep learning
Diana Mindroc-Filimon, Dominic Helmerich, Patrick Salome, Markus Sauer, Philip Kollmannsberger