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Microscopy preprints – Bioimage analysis tools

Posted by , on 5 November 2021

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

2020 BioImage Analysis Survey: Community experiences and needs for the future. Nasim Jamali, Ellen TA Dobson, Kevin W. Eliceiri, Anne E. Carpenter, Beth A. Cimini

Cell-ACDC: a user-friendly toolset embedding state-of-the-art neural networks for segmentation, tracking and cell cycle annotations of live-cell imaging data. Francesco Padovani, Benedikt Mairhörmann, Pascal Falter-Braun, Jette Lengefeld, Kurt M. Schmoller

Figure extracted from Padovani et al.

ZELDA: a 3D Image Segmentation and Parent-Child relation plugin for microscopy image analysis in napari. Rocco D’Antuono, Giuseppina Pisignano

Blind deconvolution in autocorrelation inversion for multi-view light sheet microscopy. Elena Corbetta, Alessia Candeo, Andrea Bassi, Daniele Ancora

Figure extracted from Corbetta et al.

DeepBacs: Bacterial image analysis using open-source deep learning approaches. Christoph Spahn, Romain F. Laine, Pedro Matos Pereira, Estibaliz Gómez-de-Mariscal, Lucas von Chamier, Mia Conduit, Mariana G Pinho, Séamus Holden, Guillaume Jacquemet, Mike Heilemann, Ricardo Henriques

Figure extracted from Spahn et al.

Bayesian machine learning analysis of single-molecule fluorescence colocalization images. Yerdos A. Ordabayev, Larry J. Friedman, Jeff Gelles, Douglas L. Theobald

Figure extracted from Ordabayev et al.

DetecDiv, a deep-learning platform for automated cell division tracking and replicative lifespan analysis. Théo Aspert, Didier Hentsch, Gilles Charvin

Vesalius: high-resolution in silico anatomization of Spatial Transcriptomic data using Image Analysis. Patrick C.N. Martin, Cecilia Lövkvist, Byung-Woo Hong, Kyoung Jae Won

Figure extracted from Martin et al.

An open-source method for analysis of confocal calcium imaging with sparse cells. Alisa A. Omelchenko, Lina Ni

Content-aware frame interpolation (CAFI): Deep Learning-based temporal super-resolution for fast bioimaging. Martin Priessner, David C.A. Gaboriau, Arlo Sheridan, Tchern Lenn, Jonathan R. Chubb, Uri Manor, Ramon Vilar Compte, Romain F. Laine

Figure extracted from Priessner et al.

YeastMate: Neural network-assisted segmentation of mating and budding events in S. cerevisiae. David Bunk, Julian Moriasy, Felix Thoma, Christopher Jakubke, Christof Osman, David Hörl

Mistic: an open-source multiplexed image t-SNE viewer. Sandhya Prabhakaran, Chandler Gatenbee, Mark Robertson-Tessi, Jeffrey West, Amer A. Beg, Jhanelle Gray, Scott Antonia, Robert A. Gatenby, Alexander R. A. Anderson

Figure extracted from Prabhakaran et al.

Labkit: Labeling and Segmentation Toolkit for Big Image Data. Matthias Arzt, Joran Deschamps, Christopher Schmied, Tobias Pietzsch, Deborah Schmidt, Robert Haase, Florian Jug

Figure extracted from Arzt et al.

PySOFI: an open source Python package for SOFI. Yuting Miao, Shimon Weiss, Xiyu Yi

RS-FISH: Precise, interactive, fast, and scalable FISH spot detection. Ella Bahry, Laura Breimann, Marwan Zouinkhi, Leo Epstein, Klim Kolyvanov, Xi Long, Kyle I S Harrington, Timothée Lionnet, Stephan Preibisch

Figure extracted from Bahry et al.
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