Microscopy preprints – bioimage analysis

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

AI-directed voxel extraction and volume EM identify intrusions as sites of mitochondrial contact
Benjamin S. Padman, Runa Lindblom, Michael Lazarou

Quantifying the nuclear localisation of fluorescently tagged proteins
Julien Hurbain, Pieter Rein ten Wolde, Peter S. Swain

Sparse Annotation is Sufficient for Bootstrapping Dense Segmentation
Vijay Venu Thiyagarajan, Arlo Sheridan, Kristen M. Harris, Uri Manor

SpotMAX: a generalist framework for multi-dimensional automatic spot detection and quantification
Francesco Padovani, Ivana Čavka, Ana Rita Rodrigues Neves, Cristina Piñeiro López, Nada Al-Refaie, Leonardo Bolcato, Dimitra Chatzitheodoridou, Yagya Chadha, Xiaofeng A. Su, Jette Lengefeld, Daphne S. Cabianca, Simone Köhler, Kurt M. Schmoller

CelFDrive: Artificial Intelligence assisted microscopy for automated detection of rare events
Scott Brooks, Sara Toral-Pérez, David S. Corcoran, Karl Kilborn, Brian Bodensteiner, Hella Baumann, Nigel J. Burroughs, Andrew D. McAinsh, Till Bretschneider

inTRACKtive — A Web-Based Tool for Interactive Cell Tracking Visualization
Teun A.P.M. Huijben, Ashley G. Anderson III, Andrew Sweet, Erin Hoops, Connor Larsen, Kyle Awayan, Jordão Bragantini, Chi-Li Chiu, Loïc A. Royer

Towards Transparency and Knowledge Exchange in AI-assisted Data Analysis Code Generation Creators
Haase, Robert

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

An integrative spatial multi-omic workflow for unified analysis of tumor tissue
Jurgen Kriel, Joel J.D. Moffet, Tianyao Lu, Oluwaseun E. Fatunla, Vinod K. Narayana, Adam Valkovic, Ana Maluenda, Malcolm J. McConville, Ellen Tsui, James R. Whittle, Sarah A. Best, Saskia Freytag

BiaPy: Accessible deep learning on bioimages
Daniel Franco-Barranco, Jesuś A. Andrés-San Román, Ivan Hidalgo-Cenalmor, Lenka Backová, Aitor González-Marfil, Clément Caporal, Anatole Chessel, Pedro Gómez-Gálvez, Luis M. Escudero, Donglai Wei, Arrate Muñoz-Barrutia, Ignacio Arganda-Carreras

VNC-Dist: A machine learning-based tool for quantification of neuronal positioning in the ventral nerve cord of C. elegans
Saber Saharkhiz, Mearhyn Petite, Tony Roenspies, Theodore Perkins, Antonio Colavita

TissueViewer: A Web-Based Multiplexed Image Viewer
D.G.P. van IJzendoorn, M. Matusiak, R.B. West, M. van de Rijn

Deep learning-based cytoskeleton segmentation for accurate high-throughput measurement of cytoskeleton density
Ryota Horiuchi, Asuka Kamimura, Yuga Hanaki, Hikari Matsumoto, Minako Ueda, Takumi Higaki

Biom3d, a modular framework to host and develop 3D segmentation methods
Guillaume Mougeot, Sami Safarbati, Hervé Alégot, Pierre Pouchin, Nadine Field, Sébastien Almagro, Émilie Pery, Aline Probst, Christophe Tatout, David E. Evans, Katja Graumann, Frédéric Chausse, Sophie Desset

3DCellComposer – A Versatile Pipeline Utilizing 2D Cell Segmentation Methods for 3D Cell Segmentation
Haoran Chen, Robert F. Murphy

Automated cell detection for immediate early gene-expressing neurons using inhomogeneous background subtraction in fluorescent images
Hisayuki Osanai, Mary Arai, Takashi Kitamura, Sachie K Ogawa

Kaizen: Decomposing cellular images with VQ-VAE
Daniel Majoral, Marharyta Domnich

Cell-context dependent in silico organelle localization in label-free microscopy images
Nitsan Elmalam, Assaf Zaritsky

µPIX: Leveraging Generative AI for Enhanced, Personalized and Sustainable Microscopy
Gabriel Bon, Daniel Sapède, Cédric Matthews, Fabrice Daian

A Deep Learning Pipeline for Mapping in situ Network-level Neurovascular Coupling in Multi-photon Fluorescence Microscopy
Matthew Rozak, James Mester, Ahmadreza Attarpour, Adrienne Dorr, Shruti Patel, Margaret Koletar, Mary Hill, JoAnne McLaurin, Maged Goubran, Bojana Stefanovic

Automated segmentation of soft X-ray tomography: native cellular structure with sub-micron resolution at high throughput for whole-cell quantitative imaging in yeast
Jianhua Chen, Mary Mirvis, Axel Ekman, Bieke Vanslembrouck, Mark Le Gros, Carolyn Larabell, Wallace F. Marshall

Annotating CryoET Volumes: A Machine Learning Challenge
Ariana Peck, Yue Yu, Jonathan Schwartz, Anchi Cheng, Utz Heinrich Ermel, Saugat Kandel, Dari Kimanius, Elizabeth Montabana, Daniel Serwas, Hannah Siems, Feng Wang, Zhuowen Zhao, Shawn Zheng, Matthias Haury, David Agard, Clinton Potter, Bridget Carragher, Kyle Harrington, Mohammadreza Paraan

bia-binder: A web-native cloud compute service for the bioimage analysis community
Craig T. Russell, Jean-Marie Burel, Awais Athar, Simon Li, Ugis Sarkans, Jason Swedlow, Alvis Brazma, Matthew Hartley, Virginie Uhlmann

Cascaded Diffusion Models for 2D and 3D Microscopy Image Synthesis to Enhance Cell Segmentation
Rüveyda Yilmaz, Kaan Keven, Yuli Wu, Johannes Stegmaier

ViTally Consistent: Scaling Biological Representation Learning for Cell Microscopy
Kian Kenyon-Dean, Zitong Jerry Wang, John Urbanik, Konstantin Donhauser, Jason Hartford, Saber Saberian, Nil Sahin, Ihab Bendidi, Safiye Celik, Marta Fay, Juan Sebastian Rodriguez Vera, Imran S Haque, Oren Kraus

Segment Anything for Dendrites from Electron Microscopy
Zewen Zhuo, Ilya Belevich, Ville Leinonen, Eija Jokitalo, Tarja Malm, Alejandra Sierra, Jussi Tohka

A metric embedding kernel for live cell microscopy signaling patterns
Layton Aho, Mark Winter, Marc DeCarlo, Agne Frismantiene, Yannick Blum, Paolo Armando Gagliardi, Olivier Pertz, Andrew R. Cohen

Enhancing Research Through Image Analysis Workshops: Experiences and Best Practices
Stefania Marcotti, Martin L. Jones, Thomas J. A. Slater, David Barry

Logic-based machine learning predicts how escitalopram inhibits cardiomyocyte hypertrophy
Taylor G. Eggertsen, Joshua G. Travers, Elizabeth J. Hardy, Matthew J. Wolf, Timothy A. McKinsey, View ORCID ProfileJeffrey J. Saucerman

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