Oufti is a stand-alone open source software package designed to perform semi-automated sub-pixel precision detection and quantification of microbial cells from phase-contrast microscopy images. It can handle confluent cell samples and is scalable for high-throughput analysis of large datasets. The software also provides tools for quantitative analysis of both diffraction- and non-diffraction-limited fluorescent signals. Its GUI is interactive and includes post-processing functions for primary data analysis.Download Oufti.

MicrobeTracker is an earlier version of Oufti. The software package requires MATLAB for use.






Analysis code used in our publications


Jutras BL, Scott M, Parry B, Biboy J, Gray J, Vollmer W, Jacobs-Wagner C. Lyme disease and relapsing fever Borrelia elongate through zones of peptidoglycan synthesis that mark division sites of daughter cells PNAS 2016 113 (33) 9162-9170