NAISS
SUPR
NAISS Projects
SUPR
Deep learning based species classification of bacteria using time-lapse of growth in microfluidic chip imaged by phase contrast microscopy
Dnr:

NAISS 2025/23-590

Type:

NAISS Small Storage

Principal Investigator:

Erik Hallström

Affiliation:

Uppsala universitet

Start Date:

2025-10-13

End Date:

2026-10-01

Primary Classification:

10207: Computer graphics and computer vision (System engineering aspects at 20208)

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. In this final year, we aim to extend the method to clinical patient isolates. Alvis has been properly acknowledged in all our previous publications (mentioned in the activity reports).