DeepBacs for multi-task bacterial image analysis using open-source deep learning approaches

Christoph Spahn, Estibaliz Gómez-de-Mariscal, Romain F Laine, Pedro M Pereira, Lucas von Chamier, Mia Conduit, Mariana G Pinho, Guillaume Jacquemet, Séamus Holden, Mike Heilemann, Ricardo Henriques

Research output: Contribution to journalArticleScientificpeer-review

Abstract

This work demonstrates and guides how to use a range of state-of-the-art artificial neural-networks to analyse bacterial microscopy images using the recently developed ZeroCostDL4Mic platform. We generated a database of image datasets used to train networks for various image analysis tasks and present strategies for data acquisition and curation, as well as model training. We showcase different deep learning (DL) approaches for segmenting bright field and fluorescence images of different bacterial species, use object detection to classify different growth stages in time-lapse imaging data, and carry out DL-assisted phenotypic profiling of antibiotic-treated cells. To also demonstrate the ability of DL to enhance low-phototoxicity live-cell microscopy, we showcase how image denoising can allow researchers to attain high-fidelity data in faster and longer imaging. Finally, artificial labelling of cell membranes and predictions of super-resolution images allow for accurate mapping of cell shape and intracellular targets. Our purposefully-built database of training and testing data aids in novice users' training, enabling them to quickly explore how to analyse their data through DL. We hope this lays a fertile ground for the efficient application of DL in microbiology and fosters the creation of tools for bacterial cell biology and antibiotic research.

Original languageEnglish
Article number688
Number of pages18
JournalCommunications biology
Volume5
Issue number1
DOIs
Publication statusPublished - 9 Jul 2022
MoE publication typeA1 Journal article-refereed

Keywords

  • Anti-Bacterial Agents/pharmacology
  • Deep Learning
  • Diagnostic Imaging
  • Image Processing, Computer-Assisted/methods
  • Neural Networks, Computer

Fingerprint

Dive into the research topics of 'DeepBacs for multi-task bacterial image analysis using open-source deep learning approaches'. Together they form a unique fingerprint.

Cite this