Microscopy preprints – bioimage analysis tools

Posted by , on 1 March 2023

Here is a curated selection of preprints published recently. In this post, we focus specifically on new bioimage analysis tools, including an introduction to quantification of microscopy data from Siân Culley and colleagues.

Zero-shot learning enables instant denoising and super-resolution in optical fluorescence microscopy
Chang Qiao, Yunmin Zeng, Quan Meng, Xingye Chen, Haoyu Chen, Tao Jiang, Rongfei Wei, Jiabao Guo, Wenfeng Fu, Huaide Lu, Di Li, Yuwang wang, Hui Qiao, Jiamin Wu, Dong Li, Qionghai Dai

Figure extracted from Qiao, et al.

Active mesh and neural network pipeline for cell aggregate segmentation
Matthew B. Smith, Hugh Sparks, Jorge Almagro, Agathe Chaigne, Axel Behrens, Chris Dunsby, Guillaume Salbreux

Figure extracted from Smith, et al.

DeepD3, an Open Framework for Automated Quantification of Dendritic Spines
Martin H P Fernholz, Drago A Guggiana Nilo, Tobias Bonhoeffer, Andreas M Kist

Figure extracted from Fernholz, et al.

Efficient image analysis for large-scale next generation histopathology using pAPRica
Jules Scholler, Joel Jonsson, Tomás Jordá-Siquier, Ivana Gantar, Laura Batti, Bevan L. Cheeseman, Stéphane Pagès, Ivo F. Sbalzarini, Christophe M. Lamy

Figure extracted from Scholler, et al.

Artificial channel separation of monochrome multi-structure microscopy image
Luhong Jin, Jingfang Liu, Heng Zhang, Yunqi Zhu, Haixu Yang, Jianhang Wang, Luhao Zhang, Yingke Xu

Figure extracted from Jin, et al.

Ensemble Processing and Synthetic Image Generation for Abnormally Shaped Nuclei Segmentation
Yue Han, Yang Lei, Viktor Shkolnikov, Daisy Xin, Alicia Auduong, Steven Barcelo, Jan Allebach, Edward J. Delp

Figure extracted from Han, et al.

Deep-Learning Assisted, Single-molecule Imaging analysis (Deep-LASI) of multi-color DNA Origami structures
Simon Wanninger, Pooyeh Asadiatouei, Johann Bohlen, Clemens-Bässem Salem, Philip Tinnefeld, Evelyn Ploetz, Don C. Lamb

A simple image processing pipeline to sharpen topology maps in multi-wavelength interference microscopy
Peter W. Tinning, Jana K. Schniete, Ross Scrimgeour, Lisa S. Kölln, Liam M. Rooney, Trevor J. Bushell, Gail McConnell

Figure extracted from Tinning, et al.

Label-Free Mammalian Cell Tracking Enhanced by Precomputed Velocity Fields
Yue Han, Yang Lei, Viktor Shkolnikov, Daisy Xin, Steven Barcelo, Jan Allebach, Edward J. Delp

FriendlyClearMap: An optimized toolkit for mouse brain mapping and analysis
Moritz Negwer, Bram Bosch, Maren Bormann, Rick Hesen, Lukas Lütje, Lynn Aarts, Carleen Rossing, Nael Nadif Kasri, Dirk Schubert

Figure extracted from Negwer, et al.

Small Training Dataset Convolutional Neural Networks for Application Specific Super-Resolution Microscopy
Varun Mannam, Scott Howard

Quantifying yeast microtubules and spindles using the Toolkit for Automated Microtubule Tracking (TAMiT)
Saad Ansari, Zachary R. Gergely, Patrick Flynn, Gabriella Li, Jeffrey K. Moore, Meredith D. Betterton

Made to measure: an introduction to quantification in microscopy data
Siân Culley, Alicia Cuber Caballero, Jemima J Burden, Virginie Uhlmann

Figure extracted from Culley, et al.

Culley and colleagues

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