Software

Tools I have written or contributed to for analysing bacterial growth — in plate readers, microfluidic chambers and bioreactors. Everything linked here is on GitHub.

FriendChip

Python

image analysis

microfluidics

author

Config-first Python pipeline for microfluidics timelapse image analysis — from raw Leica .lif and Nikon .nd2 files through segmentation, tracking and lineage reconstruction to growth rates, dose–response curves and spatial cross-feeding analytics. Omnipose segmentation with GPU acceleration; one JSON config per experiment, one CLI and web app to drive every stage.

plate-functions

growth curves

plate reader

author

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.