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Microscopy preprints – Bioimage analysis tools

Posted by , on 17 December 2021

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

Robust and unbiased estimation of the background distribution for automated quantitative imaging. Mauro Silberberg, Hernán E. Grecco

Figure extracted from Silberberg et al.

Real-time Image Denoising of Mixed Poisson-Gaussian Noise in Fluorescence Microscopy Images using ImageJ. Varun Mannam, Yide Zhang, Yinhao Zhu, Evan Nichols, Qingfei Wang, Vignesh Sundaresan, Siyuan Zhang, Cody Smith, Paul W Bohn, Scott Howard

Figure extracted from Mannam et al.

Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation. Kevin J. Cutler, Carsen Stringer, Paul A. Wiggins, Joseph D. Mougous

Figure extracted from Cutler et al.

Evaluation of cell segmentation methods without reference segmentations. Haoran Chen, Robert F. Murphy

Figure extracted from Chen et al.

An end-to-end workflow for multiplexed image processing and analysis. Jonas Windhager, Bernd Bodenmiller, Nils Eling

Figure extracted from Windhager et al.

HARLEY: A Semi-Automated detection of foci in fluorescence images of yeast. Ilya Shabanov, J. Ross Buchan

Figure extracted from Shabanov et al.

VALIS: Virtual Alignment of pathoLogy Image Series. Chandler D. Gatenbee, Ann-Marie Baker, Sandhya Prabhakaran, Robbert J. C. Slebos, Gunjan Mandal, Eoghan Mulholland, Simon Leedham, Jose R. Conejo-Garcia, Christine H. Chung, Mark Robertson-Tessi, Trevor A. Graham, Alexander R.A. Anderson

Figure extracted from Gatenbee et al.

The annotation and analysis of complex 3D plant organs using 3DCoordX. Athul Vijayan, Soeren Strauss, Rachele Tofanelli, Tejasvinee Atul Mody, Karen Lee, Miltos Tsiantis, Richard S Smith, Kay Schneitz

Figure extracted from Vijayan et al.

LiveCellMiner: A New Tool to Analyze Mitotic Progression. Daniel Moreno-Andrés, Anuk Bhattacharyya, Anja Scheufen, Johannes Stegmaier

Figure extracted from Moreno-Andrés et al.

Spacemake: processing and analysis of large-scale spatial transcriptomics data. Tamas Ryszard Sztanka-Toth, Marvin Jens, Nikos Karaiskos, Nikolaus Rajewsky

Figure extracted from Sztanka-Toth et al.

Image-based representation of massive spatial transcriptomics datasets. Stephan Preibisch, Nikos Karaiskos, Nikolaus Rajewsky

Figure extracted from Preibisch et al.

DeepSpot: a deep neural network for RNA spot enhancement in smFISH microscopy images. Emmanuel Bouilhol, Edgar Lefevre, Benjamin Dartigues, Robyn Brackin, Anca Flavia Savulescu, Macha Nikolski

Figure extracted from Bouilhol et al.

A deep learning framework for quantitative analysis of actin microridges. Rajasekaran Bhavna, Mahendra Sonawane

Figure extracted from Bhavna et al.

DeepProjection: Rapid and structure-specific projections of tissue sheets embedded in 3D microscopy stacks using deep learning. Daniel Haertter, Xiaolei Wang, Stephanie M. Fogerson, Nitya Ramkumar, Janice M. Crawford, Kenneth D. Poss, Stefano Di Talia, Daniel P. Kiehart, Christoph F. Schmidt

Figure extracted from Haertter et al.

Isotropic Reconstruction of Electron Tomograms with Deep Learning. Yun-Tao Liu, Heng Zhang, Hui Wang, Chang-Lu Tao, Guo-Qiang Bi, Z. Hong Zhou

Figure extracted from Liu et al.

Contour, a semi-automated segmentation and quantitation tool for cryo-soft-X-ray tomography. Kamal L Nahas, João Ferreira Fernandes, Colin Crump, Stephen Graham, Maria Harkiolaki

Figure extracted from Nahas et al.

OpenCell: proteome-scale endogenous tagging enables the cartography of human cellular organization. Nathan H. Cho, Keith C. Cheveralls, Andreas-David Brunner, Kibeom Kim, André C. Michaelis, Preethi Raghavan, Hirofumi Kobayashi, Laura Savy, Jason Y. Li, Hera Canaj, James Y.S. Kim, Edna M. Stewart, Christian Gnann, Frank McCarthy, Joana P. Cabrera, Rachel M. Brunetti, Bryant B. Chhun, Greg Dingle, Marco Y. Hein, Bo Huang, Shalin B. Mehta, Jonathan S. Weissman, Rafael Gómez-Sjöberg, Daniel N. Itzhak, Loic A. Royer, Matthias Mann, Manuel D. Leonetti

Figure extracted from Cho et al.

Mars, a molecule archive suite for reproducible analysis and reporting of single molecule properties from bioimages. Nadia M Huisjes, Thomas M Retzer, Matthias J Scherr, Rohit Agarwal, Barbara Safaric, Anita Minnen, Karl E Duderstadt

Figure extracted from Huisjes et al.

BioImageIT: Open-source framework for integration of image data-management with analysis. Sylvain Prigent, Cesar Augusto Valades-Cruz, Ludovic Leconte, Leo Maury, Jean Salamero, Charles Kervrann

Figure extracted from Prigent et al.
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