Microscopy preprints – bioimage analysis tools

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

NanoPyx: super-fast bioimage analysis powered by adaptive machine learning
Bruno M. Saraiva, Inês M. Cunha, António D. Brito, Gautier Follain, Raquel Portela, Robert Haase, Pedro M. Pereira, Guillaume Jacquemet, Ricardo Henriques

napari-threedee: a toolkit for human-in-the-loop 3D image analysis in napari
Kevin A. Yamauchi, Alister Burt

Deep learning permits imaging of multiple structures with the same fluorophores
Luhong Jin, Jingfang Liu, Heng Zhang, Yunqi Zhu, Haixu Yang, Jianhang Wang, Luhao Zhang, Yingke Xu, Cuifang Kuang, Xu Liu

Image Denoising and the Generative Accumulation of Photons
Alexander Krull, Hector Basevi, Benjamin Salmon, Andre Zeug, Franziska Müller, Samuel Tonks, Leela Muppala, Ales Leonardis

Multi-color live-cell optical nanoscopy using phasor analysis
Zhimin Zhang, Yuran Huang, Wenli Tao, Yunfei Wei, Liang Xu, Wenwen Gong, Yuhui Zhang, Jiaqiang Zhou, Liangcai Cao, Yong Liu, Yubing Han, Cuifang Kuang, Xu Liu

OrgaMapper: A robust and easy-to-use workflow for analyzing organelle positioning
Christopher Schmied, Michael Ebner, Paula Samsó Ferré, Volker Haucke, Martin Lehmann

Resolution enhancement with deblurring by pixel reassignment (DPR)
Bingying Zhao, Jerome Mertz

Coordinate-based neural representations for computational adaptive optics in widefield microscopy
Iksung Kang, Qinrong Zhang, Stella X. Yu, Na Ji

Augmented Super-Resolution Radial Fluctuations (aSRRF) Pushing the Limits of Structured Illumination Microscopy
Heng Zhang, Jianhang Wang, Luhong Jin, Yunqi Zhu, Yuting Guo, Meng Zhang, Yuhui Zhang, Zhixiong Wang, Yisun Su, Yicong Wu, Baohua Ji, Derek Toomre, Xu Liu, Yingke Xu

EMDiffuse: a diffusion-based deep learning method augmenting ultrastructural imaging and volume electron microscopy
Chixiang Lu, Kai Chen, Heng Qiu, Xiaojun Chen, Gu Chen, Xiaojuan Qi, Haibo Jiang

CartoCell, a high-content pipeline for accurate 3D image analysis, unveils cell morphology patterns in epithelial cysts
Jesús A. Andrés-San Román, Carmen Gordillo-Vázquez, Daniel Franco-Barranco, Laura Morato, Cecilia H. Fernández-Espartero, Gabriel Baonza, Antonio Tagua, Pablo Vicente-Munuera, Ana M. Palacios, María P. Gavilán, Fernando Martín-Belmonte, Valentina Annese, Pedro Gómez-Gálvez, Ignacio Arganda-Carreras, Luis M. Escudero

DLSIA: Deep Learning for Scientific Image Analysis
Eric J Roberts, Tanny Chavez, Alexander Hexemer, Petrus H. Zwart

CellProfiler plugins — an easy image analysis platform integration for containers and Python tools
Erin Weisbart, Callum Tromans-Coia, Barbara Diaz-Rohrer, David R Stirling, Fernanda Garcia-Fossa, Rebecca A Senft, Mark C Hiner, Marcelo B de Jesus, Kevin W Eliceiri, Beth A Cimini

A Survey on Training Challenges in Generative Adversarial Networks for Biomedical Image Analysis
Muhammad Muneeb Saad, Ruairi O’Reilly, Mubashir Husain Rehmani

From Pixels to Phenotypes: Integrating Image-Based Profiling with Cell Health Data Improves Interpretability
Srijit Seal, Jordi Carreras-Puigvert, Anne E Carpenter, Ola Spjuth, Andreas Bender

CytoPb: Segmentation-free and threshold-free analysis of highly multiplexed images of biological tissue
Paul R Barber, Luigi Dolcetti, Chen-An Yeh, Tony Ng

GreenMemTraX: A User-Friendly Software for Super-Resolution Analysis of Membrane Protein Dynamics and Nanoscale Organization in Plants
Leander Rohr, Alexandra Ehinger, Luiselotte Rausch, Nina Glöckner Burmeister, Alfred J. Meixner, Klaus Harter, Birgit Kemmerling, Sven zur Oven-Krockhaus

Per-pixel unmixing of spectrally overlapping fluorophores using intra-exposure excitation modulation
Hana Valenta, Franziska Bierbuesse, Raffaele Vitale, Cyril Ruckebusch, Wim Vandenberg, Peter Dedecker

Acto3D: user- and budget-friendly software for multichannel high-resolution three-dimensional imaging
Naoki Takeshita, Shinichiro Sakaki, Rie Saba, Satoshi Inoue, Kosuke Nishikawa, Atsuko Ueyama, Kazuhiko Matsuo, Masaki Shigeta, Yoshiro Nakajima, Daisuke Kobayashi, Hideya Yamazaki, Kei Yamada, Tomoko Iehara, Kenta Yashiro

tUbe net: a generalisable deep learning tool for 3D vessel segmentation
Natalie Holroyd, Zhongwang Li, Claire Walsh, Emmeline Brown, Rebecca Shipley, Simon Walker-Samuel

Deep learning reduces data requirements and allows real-time measurements in Imaging Fluorescence Correlation Spectroscopy
Wai Hoh Tang, Shao Ren Sim, Daniel Ying Kia Aik, Ashwin Venkata Subba Nelanuthala, Thamarailingam Athilingam, Adrian Röllin, Thorsten Wohland

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