Software

Open tools for analysing bacterial growth in plate readers, microfluidic chambers and bioreactors.

Tools I have written or contributed to for analysing bacterial growth in plate readers, microfluidic chambers and bioreactors. Linked cards open the repository on GitHub. Cards marked private are not yet published.

FriendChip

Private repository

From a raw .lif/.nd2 microfluidics timelapse to single-cell growth rates, dose–response fits and cross-feeding maps. One config per experiment, one CLI, GPU segmentation and tracking.

plate-functions

R functions for 96-well plate-reader growth curves: log-linear sliding-window maximum growth rate, per-well yield / AUC / lag / carrying capacity, blank correction, time-grid sanity checks and per-plate parameter diagnostics. Shared as a git submodule across several lab projects.

ChiBio (fork)

Fork of the open-source ChiBio bioreactor platform with additions for OD dilution-series calibration, timed dosing schedules, fluorescence-assisted OD control and measurement-mutex fixes for the device’s read/write sequences.