Code

Here are some examples of code that I've been working on. They are mostly a result of my work on Single Molecule Localisation Microscopy (e.g. PALM/STORM), but I expect the approaches I've taken will be useful for other applications. The idea is to share the way I've solved problems in a way that is (hopefully) helpful to others!

Matlab and Python

• Experiments with Matlab and Python
• Calling Matlab from Python

Air Quality

• Visualising the luftdaten archive:
  • Shiny App
  • Github

Biology Lab

• Analysing plate reader data in R

Single Molecule Microscopy

• Finding single molecules with Python
• "LM": MATLAB Reconstruction Code for PALM / STORM etc.
• 2D curve fitting with R
• Finding single molecules with R
• Reading, plotting and analysing localisation microscopy data with R
• Alternative approach to plotting 2D histograms
• Simulating and identifying clusters of molecules - Shiny Web App

Infectious Disease

• A Year in Infectious Disease
• A Year in Infectious Disease - Shiny Web App
• Can search trends predict infectious disease?
• Mapping infectious disease

Other Stuff

• Lorenz equations (Chaos)
• Turing patterns