Most code is hosted on the ICR Github page. Programs can be downloaded as a .zip, or cloned using git. Feel free to contribute and submit pull requests.

Please contact adam.tyson01@icr.ac.uk for any assistance.

General scripts/macros

ImageJ/FIJI macros

Cellprofiler pipelines

MATLAB scripts

Python scripts

Bash scripts

Specific scripts/pipelines:

MATLAB

foci2D - Assess foci in 2D images on a per cell basis (using nuclear marker)

cell-coloc-3D - Measure distribution of a marker per cell, per object (manually segmented)

foci-colocalisation - Measure colocalisation of two types of foci per cell

CalciumAnalysis - Simple analysis of calcium dynamics in 2D images

foci-timelapse - Measure foci dynamics

man-seg-analysis - Analyses objects following manual segmentation (e.g. EM)

Python

coloc-3DT - Measure intensity of one marker in another

relativeTrack - Track one class of objects relative to another