Skip to content
To analyze expansion and growth dynamics of populations. File handling for Leica SP8 data export.
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Type Name Latest commit message Commit time
Failed to load latest commit information. Add files via upload Aug 14, 2019


To analyze expansion and growth dynamics of fluorescently labeld cells expanding in soft-agar. Code implements file handling specifically for the Leica Microsystems Leica Application Suite and its data export option as raw tif.

We used this code to analyze images acquired with a Leica Microsystems SP8 confocal microscope. Method details and the biological context are provided in our manuscript:

  • J.Cremer, T.Honda, Y.Tang, J.Wong-Ng, M.Vergassola, T.Hwa. Chemotaxis as a navigation strategy to thrive in nutrient-replete environments

August 2019, Jonas Cremer and all coauthors.

Required modules

Required modules include Numpy, SciPy, and PIL. This code was tested and run with Python 2.7.

Collect data

Images were collected scanning samples in low-magnification, tile-scanning along one axes (x) and through the agar (z). Ensure scans across the entire agar thickness, adjust intensity and detection settings such that full dynamical range is used but saturation at high bacterial densities (later in time) is prevented. See our manuscript for detailed informations.

Run the script

Run "" to do image analysis. Before running script the first time, adjust path settings (name of input data and output folders etc), see comments provided in the file.

You can’t perform that action at this time.