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Microscopy preprints – Bioimage analysis tools

Posted by , on 8 June 2022

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

A Hitchhiker`s Guide through the Bio-image Analysis Software Universe
Robert Haase, Elnaz Fazeli, David Legland, Michael Doube, Siân Culley, Ilya Belevich, Eija Jokitalo, Martin Schorb, Anna Klemm, Christian Tischer

A comparison of ImageJ and machine learning based image analysis methods to measure cassava bacterial blight disease severity
Kiona Elliott, Jeffrey C. Berry, Hobin Kim, Rebecca S. Bart

Figure extracted from Elliott, et al.

Single-cell tracking data aimed for big data analyses
Mónica Suárez Korsnes, Reinert Korsnes

The Image Data Explorer: interactive exploration of image-derived data
Coralie Muller, Beatriz Serrano-Solano, Yi Sun, Christian Tischer, Jean-Karim Hériché

Figure extracted from Muller et al.

MorphoFeatures: unsupervised exploration of cell types, tissues and organs in volume electron microscopy
Valentyna Zinchenko, Johannes Hugger, Virginie Uhlmann, Detlev Arendt, Anna Kreshuk

Figure extracted from Zinchenko et al.

LOMAR: LOcalization Microscopy Analysis in R
Maria Theiss, Alvis Brazma, Virginie Uhlmann, Jean-Karim Hériché

Figure extracted from Theiss et al.

Identification and calibration of ultrabright localizations to eliminate quantification error in SMLM
Bo Cao, Jielei Ni, Gang Niu, Danni Chen, Gang Liu, Lingxiao Zhou, Tingying Xia, Fu Feng, Shibiao Wei, Xiaocong Yuan, Yanxiang Ni

Visinity: Visual Spatial Neighborhood Analysis for Multiplexed Tissue Imaging Data
Simon Warchol, Robert Krueger, Ajit Johnson Nirmal, Giorgio Gaglia, Jared Jessup, Cecily C. Ritch, John Hoffer, Jeremy Muhlich, Megan L. Burger, Tyler Jacks, Sandro Santagata, Peter K. Sorger, Hanspeter Pfister

Figure extracted from Warchol et al.

DINAVID: A Distributed and Networked Image Analysis System for Volumetric Image Data
Shuo Han, Alain Chen, Soonam Lee, Chichen Fu, Changye Yang, Liming Wu, Seth Winfree, Tarek M. El-Achkar, Kenneth W. Dunn, Paul Salama, Edward J. Delp

Figure extracted from Han et al.

Instance segmentation of mitochondria in electron microscopy images with a generalist deep learning model
Ryan Conrad, Kedar Narayan

Figure extracted from Conrad and Narayan
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