Microscopy preprints – bioimage analysis

Posted by FocalPlane, on 18 October 2024

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

CellMet: Extracting 3D shape metrics from cells and tissues
Sophie Theis, Mario A Mendieta-Serrano, Bernardo Chapa-y-Lazo, Juliet Chen, Timothy E Saunders

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

FLIMPA: A versatile software for Fluorescence Lifetime Imaging Microscopy Phasor Analysis
Sofia Kapsiani, Nino F. Läubli, Edward N. Ward, Mona Shehata, Clemens F. Kaminski, Gabriele S. Kaminski Schierle

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

F-BIAS: Towards a distributed national core facility for Bioimage Analysis
Mélodie Ambroset, Marie Anselmet, Clément Benedetti, Arthur Meslin, Aurélien Maillot, Christian Rouvière, Guillaume Maucort, Marine Breuilly, Marvin Albert, Gaëlle Letort, Antonio Trullo, Volker Bäcker, Jérôme Mutterer, Fabrice Cordelières, Thierry Pécot, Minh-Son Phan, Stéphane Rigaud, Magali Feyeux, Perrine Paul-Gilloteaux, Anne-Sophie Macé, Jean-Yves Tinevez

Deep learning detection of dynamic exocytosis events in fluorescence TIRF microscopy
Hugo Lachuer, Emmanuel Moebel, Anne-Sophie Macé, Arthur Masson, Kristine Schauer, Charles Kervrann

Structural Repetition Detector: multi-scale quantitative mapping of molecular complexes through microscopy
Afonso Mendes, Bruno M. Saraiva, Guillaume Jacquemet, João I. Mamede, Christophe Leterrier, Ricardo Henriques

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

Data Release: High-Resolution Imaging and Segmentation of P7 Mouse Tissue Microarchitecture Using FIB-SEM and Machine Learning
David Ackerman, Emma Avetissian, Christopher K. E. Bleck, John A. Bogovic, Michael Innerberger, Wyatt Korff, Wei-Ping Li, Zhiyuan Lu, Alyson Petruncio, Stephan Preibisch, Wei Qiu, Jeff Rhoades, Stephan Saalfeld, Malan Silva, Eric T. Trautman, Rebecca Vorimo, Aubrey Weigel, Zhiheng Yu, Yurii Zubov, CellMap Project Team

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

Going Beyond U-Net: Assessing Vision Transformers for Semantic Segmentation in Microscopy Image Analysis
Illia Tsiporenko, Pavel Chizhov, Dmytro Fishman

CRISP: Correlation-Refined Image Segmentation Process
Jennifer K. Briggs, Erli Jin, Matthew J. Merrins, Richard K.P. Benninger

Image-based force inference by biomechanical simulation
Michiel Vanslambrouck, Wim Thiels, Jef Vangheel, Casper van Bavel, Bart Smeets, Rob Jelier

DeepPaint: A deep-learning package for Cell Painting Image Classification
Diego Luna, Erik C. Johnson, Laura L. Dunphy, Ryan McQuillen

Camera Paths, Modeling, and Image Processing Tools for ArtiaX
Utz H. Ermel, Pauline Roth, Maren Wehrheim, Deborah Moser, Achilleas S. Frangakis

Four-dimensional label-free live cell image segmentation for predicting live birth potential of mouse embryos
Taichi Kanazawa, Tatsuma Yao, Sora Takeshita, Tatsuki Hirai, Ryo Suenaga, Takahiro G Yamada, Yuta Tokuoka, Kazuo Yamagata, Akira Funahashi

Parameter-free clear image deconvolution (CLID) technique for single-frame live-cell super-resolution imaging
Fudong Xue, Wenting He, Zuo’ang Xiang, Jun Ren, Chunyan Shan, Lin Yuan, Pingyong Xu

Automated model-free analysis of cryo-EM volume ensembles with SIREn
Laurel F. Kinman, Maria V. Carreira, Barrett M. Powell, Joseph H. Davis

A browser-based platform for storage, visualization, and analysis of large-scale 3D images in HPC environments
Logan A Walker, Wei Jie Lee, Bin Duan, Menelik Weatherspoon, Ye Li, Fred Y. Shen, Mou-Chi Cheng, Xiaoman Niu, Jacob Eggerd, Bin Xie, Jimmy Hon Pong Cheng, Humphrey Xu, Xiao-Xiang Zhong, Hehai Jiang, Meng Cui, Yan Yan, Dawen Cai

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

EASI-ORC: A Pipeline for the Efficient Analysis and Segmentation of smFISH Images for Organelle-RNA Colocalization Measurements in Yeast
Shahar Garin, Liav Levavi, Jeffrey E. Gerst

CellSeg3D: self-supervised 3D cell segmentation for light-sheet microscopy
Cyril Achard, Timokleia Kousi, Markus Frey, Maxime Vidal, Yves Paychère, Colin Hofmann, Asim Iqbal, Sebastien B. Hausmann, Stéphane Pagès, Mackenzie Weygandt Mathis

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

CELL-Diff: Unified diffusion modeling for protein sequences and microscopy images
Dihan Zheng, Bo Huang

A universal and effective variational method for destriping: application to light-sheet microscopy, FIB-SEM and remote sensing images
Niklas Rottmayer, Claudia Redenbach, Florian O. Fahrbach

CelloType: A Unified Model for Segmentation and Classification of Tissue Images
Minxing Pang, Tarun Kanti Roy, Xiaodong Wu, Kai Tan

Piximi – An Images to Discovery web tool for bioimages and beyond
Levin M Moser, Nodar Gogoberidze, Andréa Papaleo, Alice Lucas, David Dao, Christoph A Friedrich, Lassi Paavolainen, Csaba Molnar, David R Stirling, Jane Hung, Rex Wang, Callum Tromans-Coia, Bin Li, Edward L Evans III, Kevin W Eliceiri, Peter Horvath, Anne E Carpenter, Beth A Cimini

Convpaint – Interactive pixel classification using pretrained neural networks
Lucien Hinderling, Guillaume Witz, Roman Schwob, Ana Stojiljković, Maciej Dobrzyński, Mykhailo Vladymyrov, Joël Frei, Benjamin Grädel, Agne Frismantiene, Olivier Pertz

A novel channel invariant architecture for the segmentation of cells and nuclei in multiplexed images using InstanSeg
Thibaut Goldsborough, Alan O’Callaghan, Fiona Inglis, Léo Leplat, Andrew Filby, Hakan Bilen, Peter Bankhead