NAISS
SUPR
NAISS Projects
SUPR
Deep learning identification of bacteria from phase contrast images
Dnr:

NAISS 2026/4-1484

Type:

NAISS Small

Principal Investigator:

Erik Hallström

Affiliation:

Uppsala universitet

Start Date:

2026-10-01

End Date:

2027-10-01

Primary Classification:

20208: Computer Vision and learning System (Computer Sciences aspects in 10207)

Allocation

Abstract

In this project, we are investigating whether it is possible to train deep learning models to identify bacterial species growing in a microfluidic trap based on their spatiotemporal division patterns. This has important implications for selecting appropriate antibiotics, reducing the use of broad-spectrum agents, and improving patient outcomes. We have previously demonstrated this approach using laboratory isolates in several publications. Now, we aim to extend the method to clinical patient isolates. We think we have a solution but need a few more months to finalize the last paper. Alvis has been properly acknowledged in all our previous publications (mentioned in the activity reports). More information: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011181 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0330265 https://www.nature.com/articles/s41746-025-01948-w