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.

Links to analysis code used in our publications can be found in the Publications. Checkout more of our analysis codes on Github.