Microscopy preprints – bioimage analysis tools

Posted by FocalPlane, on 9 February 2024

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

Polarity-JaM: An image analysis toolbox for cell polarity, junction and morphology quantification
Wolfgang Giese, Jan Philipp Albrecht, Olya Oppenheim, Emir Bora Akmeriç, Julia Kraxner, Deborah Schmidt, Kyle Harrington, Holger Gerhardt

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

A new protocol for multispecies bacterial infections in zebrafish and their monitoring through automated image analysis
Désirée A. Schmitz, Tobias Wechsler, Hongwei Bran Li, Bjoern Menze, Rolf Kümmerli

NIEND: Neuronal Image Enhancement through Noise Disentanglement
Zuo-Han Zhao, Yufeng Liu

Pseudo-spectral angle mapping for automated pixel-level analysis of highly multiplexed tissue image data
Madeleine S. Durkee, Junting Ai, Gabriel Casella, Thao Cao, Anthony Chang, Ariel Halper-Stromberg, Bana Jabri, Marcus R. Clark, Maryellen L. Giger

Self-supervision advances morphological profiling by unlocking powerful image representations
Vladislav Kim, Nikolaos Adaloglou, Marc Osterland, Flavio M. Morelli, Marah Halawa, Tim König, David Gnutt, Paula A. Marin Zapata

GPT-4V exhibits human-like performance in biomedical image classification
Wenpin Hou, Zhicheng Ji

Image processing tools for petabyte-scale light sheet microscopy data
Xiongtao Ruan, Matthew Mueller, Gaoxiang Liu, Frederik Görlitz, Tian-Ming Fu, Daniel E. Milkie, Joshua Lillvis, Alison Killilea, Eric Betzig, Srigokul Upadhyayula

An image segmentation pipeline optimized for human microglia uncovers sources of morphological diversity in Alzheimer’s disease
Robert M De Jager, Annie J Lee, Alina Sigalov, Mariko Taga

Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning
Emily Laubscher, Xuefei (Julie) Wang, Nitzan Razin, Tom Dougherty, Rosalind J. Xu, Lincoln Ombelets, Edward Pao, William Graf, Jeffrey R. Moffitt, Yisong Yue, David Van Valen

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

When the pen is mightier than the sword: semi-automatic 2 and 3D image labelling
Réka Hollandi, David Bauer, Akos Diosdi, Bálint Schrettner, Timea Toth, Dominik Hirling, Gábor Hollandi, Maria Harmati, József Molnár, Peter Horvath

The Brain Image Library: A Community-Contributed Microscopy Resource for Neuroscientists
Mariah Kenney, Iaroslavna Vasylieva, Greg Hood, Ivan Cao-Berg, Luke Tuite, Rozita Laghaei, Alan M. Watson, Alexander J. Ropelewski

Sopa: a technology-invariant pipeline for analyses of image-based spatial-omics
Quentin Blampey, Kevin Mulder, Charles-Antoine Dutertre, Margaux Gardet, Fabrice André, Florent Ginhoux, Paul-Henry Cournède

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

CryoVirusDB: A Labeled Cryo-EM Image Dataset for AI-Driven Virus Particle Picking
Rajan Gyawali, Ashwin Dhakal, Liguo Wang, Jianlin Cheng

Self-inspired learning to denoise for live-cell super-resolution microscopy
Liying Qu, Shiqun Zhao, Yuanyuan Huang, Xianxin Ye, Kunhao Wang, Yuzhen Liu, Xianming Liu, Heng Mao, Guangwei Hu, Wei Chen, Changliang Guo, Jiaye He, Jiubin Tan, Haoyu Li, Liangyi Chen, Weisong Zhao

PatternJ: an ImageJ toolset for the automated and quantitative analysis of regular spatial patterns found in sarcomeres, axons, somites, and more
Mélina Baheux Blin, Vincent Loreau, Frank Schnorrer, Pierre Mangeol

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

Efficient stripe artefact removal by a variational method: application to light-sheet microscopy, FIB-SEM and remote sensing images
Niklas Rottmayer, Claudia Redenbach, Florian Fahrbach

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, Maged Goubran, Bojana Stefanovic

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

Bridging the Gap: Integrating Cutting-edge Techniques into Biological Imaging with deepImageJ
Caterina Fuster-Barceló, Carlos García López de Haro, Estibaliz Gómez-de-Mariscal, Wei Ouyang, Jean-Christophe Olivo-Marin, Daniel Sage, Arrate Muñoz-Barrutia

CAMIL: Context-Aware Multiple Instance Learning for Cancer Detection and Subtyping in Whole Slide Images
Olga Fourkioti, Matt De Vries, Chris Bakal

BiaPy: A unified framework for versatile bioimage analysis with deep learning
Daniel Franco-Barranco, Jesús 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

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

ExoJ: an ImageJ2/Fiji plugin for automated spatiotemporal detection and analysis of exocytosis
Junjun Liu, Frederik Johannes Verweij, Guillaume Van Niel, Thierry Galli, Lydia Danglot, Philippe Bun

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

OneFlowTraX: A User-Friendly Software for Super-Resolution Analysis of Single-Molecule Dynamics and Nanoscale Organization
Leander Rohr, Alexandra Ehinger, Luiselotte Rausch, Nina Glöckner Burmeister, Alfred J. Meixner, Julien Gronnier, Klaus Harter, Birgit Kemmerling, Sven zur Oven-Krockhaus

MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography
Lorenz Lamm, Simon Zufferey, Ricardo D. Righetto, Wojciech Wietrzynski, Kevin A. Yamauchi, Alister Burt, Ye Liu, Hanyi Zhang, Antonio Martinez-Sanchez, Sebastian Ziegler, Fabian Isensee, Julia A. Schnabel, Benjamin D. Engel, Tingying Peng

A Novel, Open-Source Virtual Reality Platform for Dendritic Spine Analysis
Marike L Reimer, Sierra D Kauer, Curtis A Benson, Jared F King, Siraj Patwa, Sarah Feng, Maile A Estacion, Lakshmi Bangalore, Stephen Waxman, Andrew M Tan

Piscis: a novel loss estimator of the F1 score enables accurate spot detection in fluorescence microscopy images via deep learning
Zijian Niu, Aoife O’Farrell, Jingxin Li, Sam Reffsin, Naveen Jain, Ian Dardani, Yogesh Goyal, Arjun Raj

ThirdPeak: A flexible tool designed for the robust analysis of two- and three-dimensional (single-molecule) tracking data
Thomas Müller, Elisabeth Meiser, Markus Engstler

Enabling Global Image Data Sharing in the Life Sciences
Peter Bajcsy, Sreenivas Bhattiprolu, Katy Boerner, Beth A Cimini, Lucy Collinson, Jan Ellenberg, Reto Fiolka, Maryellen Giger, Wojtek Goscinski, Matthew Hartley, Nathan Hotaling, Rick Horwitz, Florian Jug, Anna Kreshuk, Emma Lundberg, Aastha Mathur, Kedar Narayan, Shuichi Onami, Anne L. Plant, Fred Prior, Jason Swedlow, Adam Taylor, Antje Keppler

AnNoBrainer, an Automated Annotation of Mouse Brain Images using Deep Learning
Roman Peter, Petr Hrobar, Josef Navratil, Martin Vagenknecht, Jindrich Soukup, Keiko Tsuji, Nestor X. Barrezueta, Anna C. Stoll, Renee C. Gentzel, Jonathan A. Sugam, Jacob Marcus, Danny A. Bitton

A systematic evaluation of computation methods for cell segmentation
Yuxing Wang, Junhan Zhao, Hongye Xu, Cheng Han, Zhiqiang Tao, Dongfang Zhao, Dawei Zhou, Gang Tong, Dongfang Liu, Zhicheng Ji