Colocalisation

The GDSC Colocalisation plugins provide various tools to perform colocalisation analysis. The following tools are available:

Stack Threshold Processes an image stack and applies thresholding to create a mask for each channel+frame combination. This allows thresholding to be applied to a 5D image on a per frame basis and can be used to define the signal region of each channel
Colocalisation Threshold Compares two images for correlated pixel intensities. If the two images are correlated a search is performed to identify the threshold below which the two images are not correlated
CDA Uses the Confined Displacement Algorithm (CDA) to compute the significance of colocalisation metrics (Manders coefficient and correlation coefficient).

This is a modified version of the original ImageJ CDA plugin
CDA (macro) Provides support for the CDA plugin within ImageJ macros (i.e. macro recording and execution)
Stack Correlation Analyser Processes a stack image with multiple channels. Extracts all the channels and frames and performs:
  1. Thresholding to create a mask for each channel+frame
  2. All-vs-all channel correlation within the union/intersect of the channel masks
Stack Colocalisation Analyser Processes a stack image with multiple channels. Each frame is processed separately. Extracts all the channels (collating z-stacks) and performs:
  1. Thresholding to create a mask for each channel
  2. CDA analysis of channel 1-vs-channel 2, optionally within the region defined by channel 3
Particle Overlap For all particles in a mask (defined by their unique pixel value), count the overlap with a second mask image (e.g. a second set of particles). An intensity image is used to calculate the Manders coefficient of each particle.
Particle Correlation For all particles in a mask (defined by contiguous pixels with the same value), sum the pixel intensity in two different images and then perform a correlation analysis.
Colocated Mask Create a colocated mask from two source images using the threshold or minimum display value from each image to define their image mask. The two image masks are combined using an AND or OR operator.

Supports a live preview to allow interactively setting the threshold on the source images with live mask update.

Full details of the Colocalisation plugins can be found in the Colocalisation User Manual.

Download the plugin.

For further details on GDSC ImageJ plugins please contact Alex Herbert.