Microscopy preprints – bioimage analysis

Posted by FocalPlane, on 6 September 2024

Here is a curated selection of preprints published recently. In this post, we focus specifically on bioimage analysis and data management.

A quantitative pipeline for whole-mount deep imaging and multiscale analysis of gastruloids
Alice Gros, Jules Vanaret, Valentin Dunsing-Eichenauer, Agathe Rostan, Philippe Roudot, Pierre-François Lenne, Léo Guignard, Sham Tlili

Figure extracted from Gros, *et al.* The image is made available under a CC-BY 4.0 International license.

EVE is an open modular data analysis software for event-based localization microscopy
Laura M. Weber, Koen J.A. Martens, Clément Cabriel, Joel J. Gates, Manon Albecq, Fredrik Vermeulen, Katarina Hein, Ignacio Izeddin, Ulrike Endesfelder

Figure extracted from Weber, *et al.* The image is made available under a CC-BY-NC 4.0 International license.

Sainsc: a computational tool for segmentation-free analysis of in-situ capture
Niklas Müller-Bötticher, Sebastian Tiesmeyer, Roland Eils, Naveed Ishaque

Figure extracted from Müller-Bötticher, *et al.* The image is made available under a CC-BY 4.0 International license.

DaCapo: a modular deep learning framework for scalable 3D image segmentation
William Patton, Jeff L. Rhoades, Marwan Zouinkhi, David G. Ackerman, Caroline Malin-Mayor, Diane Adjavon, Larissa Heinrich, Davis Bennett, Yurii Zubov, CellMap Project Team, Aubrey V. Weigel, Jan Funke

Figure extracted from Patton, et al. The image is made available under a CC-BY 4.0 International license.

Fast and long-term super-resolution imaging of ER nano-structural dynamics in living cells using a neural network
Johanna V. Rahm, Ashwin Balakrishnan, Maren Wehrheim, Alexandra Kaminer, Marius Glogger, Laurell F. Kessler, Matthias Kaschube, Hans-Dieter Barth, Mike Heilemann

Figure extracted from Rahm, *et al.* The image is made available under a CC-BY-NC 4.0 International license.

PyPlaque: an Open-source Python Package for Phenotypic Analysis of Virus Plaque Assays
Trina De, Vardan Andriasyan, Artur Yakimovich

Cecelia: a multifunctional image analysis toolbox for decoding spatial cellular interactions and behaviour
Dominik Schienstock, Jyh Liang Hor, Sapna Devi, Scott N. Mueller

FourierMIL: Fourier filtering-based multiple instance learning for whole slide image analysis
Yi Zheng, Harsh Sharma, Margrit Betke, Jennifer E. Beane, Vijaya B. Kolachalama

Novel high-content and open-source image analysis tools for profiling mitochondrial morphology in neurological cell models
Marcus Y. Chin, David A. Joy, Madhuja Samaddar, Anil Rana, Johann Chow, Takashi Miyamoto, Meredith Calvert

CRISP: Correlation-Refined Image Segmentation Process
Jennifer K. Briggs, Erli Jin, Matthew J. Merrins, Richard K.P. Benninger

TissueViewer: A Web-Based Multiplexed Image Viewer
D.G.P. van IJzendoorn, M. Matusiak, R.B. West, M. van de Rijn

Image retrieval based on closed-loop visual–semantic neural decoding
Ryohei Fukuma, Takufumi Yanagisawa, Hidenori Sugano, Kentaro Tamura, Satoru Oshino, Naoki Tani, Yasushi Iimura, Hui Ming Khoo, Hiroharu Suzuki, Huixiang Yang, Takamitsu Iwata, Madoka Nakajima, Shinji Nishimoto, Yukiyasu Kamitani, Haruhiko Kishima

3D-Aligner: An advanced computational tool designed to correct image distortion in expansion microscopy for precise 3D reconstitution and quantitative analysis
Jonathan Loi, Dhaval Ghone, Xiaofei Qu, Aussie Suzuki

Live Cell Painting: image-based profiling in live cells using Acridine Orange
Fernanda Garcia-Fossa, Thaís Moraes-Lacerda, Mariana Rodrigues-da-Silva, Barbara Diaz-Rohrer, Shantanu Singh, Anne E. Carpenter, Beth A. Cimini, Marcelo Bispo de Jesus

An Image Processing Tool for Automated Quantification of Bacterial Burdens in Zebrafish Larvae
Naoya Yamaguchi, Hideo Otsuna, Michal Eisenberg-Bord, Lalita Ramakrishnan