Data Sets

  • Measuring Bacterial Growth | A series of fluorescence and phase contrast images of E. coli cells growing on a rich medium substrate.

  • Testing The French Flag Model| Brightfield images of developing Drosophila embryos with different dosages of the Bicoid morphogen. Also download a csv file containing more dosages from Thomas Gregor.

  • Example Images lacI titration | Example brightfield and fluorescence images of E. coli cells for the gene expression measurement analysis.

  • LacI Titration | Brightfield and fluorescence images of E. coli cells containing different numbers of transcriptional repressor molecules. Also download the .csv file of fold-change data from Garcia and Phillips 2011.

  • Measuring Cytoskeletal Filament Length Distributions | Fluorescence images of actin filaments prepared in vitro during Physiology 2016.

  • Timing Transcription in Drosophila | This data set from Hernan Garcia’s lab contains images from two developing Drosophila embryos in which either the 5’ or 3’ end of the hunchback morphogen mRNA is labeled with MS2.


The code we write in class will be added here as the course progresses.

  • Integrating Cell Division by the Euler Method | Here, we get introduced to the MATLAB programming language and learn how to numerically solve the differential growth equation. pdf

  • How the Fly Gets Its Neck | In this tutorial we go through the theory and analysis of the cephalic furrow positioning in the fly embryo. html | mlx

  • Measuring Growth Rate Through Microscopy | We’ve all (probably) measured bacterial growth by recording the OD of growing cultures. In this script, we analyze a time-lapse microscopy data set by measuring the bacterial area as a function of time. | in-class code | data set

  • Timing Transcription in Drosophila embryos | Using some of the image processing skill we learned while processing the growth movie, we measure the rate of transcription of the hunchback gene. html | mlx

  • Nonlinear Regression | We performed a nonlinear regression of our LacI titration data to estimate the best fit value for the binding energy of a repressor to the DNA.

  • Cytoskeleton length distribution | Data analysis of cytoskeleton images to obtain the length distribution and compare it with the theoretical predictions from the chemical master equation model. html | mlx

Advance Matlab tutorial (introduction to Bayesian inference)

  • Intro to Bayesian inference | First exposition to the concept of Bayesian parameter inference. [ html ] | [ mlx ] | [ raw data ]

  • Intro to Markov Chain Monte Carlo sampling | Introduction to the powerful MCMC techniques widely used for Bayesian analysis. [ html ] | [ mlx ]

Extra Tutorials

We have written several more in-depth tutorials on programming in the MATLAB programming language and have posted them below. More will be posted as the course progresses.

External Resources

Below is a list of useful online resources for learning the some principles of programming and scientific data analysis using the Python language.