Update: this plugin now supports time-series data. See the webpage for details.
I’ve been developing a new ImageJ plugin for colocalization and spatial correlation, Colocalization by Cross Correlation. For those familiar with it, the implementation is conceptually similar to Van Steensel’s CCF, but implemented quite differently in that it analyzes cross-correlation along all axes instead of just the x-axis, and uses Costes randomization to provide a measure of confidence in the correlation. Additionally, my plugin is able to generate images of the strongest correlating particles/signal from the original images. Currently, the plugin works on 2D and 3D images, though I hope to implement support for time-lapse data in the near future, where the plugin will generate a heatmap of cross-correlation over time.
I’ve posted about this plugin before, when it was early in its development, but I’ve recently gotten the plugin to a much better state (faster, more robust, better results). The plugin is available on the ImageJ update sites under the Help > Update… menu. Once installed you can find it under the Analyze > Colocalization menu. You can see the plugin webpage for a more detailed description of what it does and how to use it: Colocalization by Cross Correlation
I would appreciate any feedback you have about the plugin or the webpage, despite developing this plugin I do not have a lot of good data to test it with, so it would be great to see other people’s results. Hope some of you find this useful.
Some images of the output for those interested (taken from the webpage):