OBCOL: Organelle Based Colocalisation

Image Sets

Warning! The some of the pre-releases of the 1.45 update to ImageJ seemed to cause OBCOL problems.

The current release of 1.45 seems to be ok now, but please let us know if you experience problems.

This is the home page of the OBCOL project for organelle based colocalisation from whole cell fluorescent imaging.


OBCOL is software designed to perform organelle based colocalisation analysis from multi-fluorophore microscopy 2D, 3D and 4D cell imaging.
It is implemented as an ImageJ plugin, and source code is included in the distribution jar file.


  • Segmentatation of 2D, 3D and 4D imaging via watershedding

  • The number of fluorophore channels analysed is limited only by computer memory

  • A wide variety of colocalisation methods may be applied to quantitate the discrete objects found

  • Quantation of objects such as: position, size, number of component objects, degree of overlap between channels

  • Several visualisation methods to view the objects found
More information may be found in the User Manual on the download page and the publication referenced below.


Automated organelle-based colocalisation in whole cell imaging, B. Woodcroft, L. Hammond, J.Stow & N. Hamilton, Cytometry A, 75(11), 941-950.

(c) 2009 Nicholas Hamilton. All rights reserved.