On / Off Target Integration Automation - Help!


For my research I am looking to analyse On / off target intergration into my cell line using a reference signal as my ‘on’ target. I am a novice using ImageJ/Fiji and do not know where to start with this.

Is there a plugin/script where I could set a certain colour as my reference (green) and automatically assess another colour (red) as my integration within a certain radius of the reference signal? Additionally I would like the program to assess the off target integration as having a red signal outside the radius of the reference signal.

Ultimately I would like to automate this procedure using the macros function, this seems fairly easy once I know how to get the analysis I want.

Any help / links to resources that would help me resolve this situation would be greatly appreciated.

Many thanks,


Welcome to the forum, @hendera03!

There are many ways to correlate information from two channels, be it spot-like signals or extended objects, 2D images or 3D+time stacks. It would certainly help if you upload an example image illustrating your problem, so that others can comment more specifically.