To use the plugin

• Download Colocalization_Colormap_.jar, and place the file in the ImageJ plugin folder
• Run ImageJ
• Open desired images (must be coded in either 8-bit or 16-bit gray scale)
• Run "Colocalization" from the plugin menu
• Choose your channels from the list of open images
• Check 'Save nMDPs' option (if necessary)
• Check 'Autothreshold' option or specify your own threshold for each channel
• Finally press OK

The plugin operates on both single images and stacks. Using ''Generate color bar" you may create a color scale bar, which is a useful tool when demonstrating and interpreting results. In case of any questions or problems, run "Help and documentation" and you will be redirected to this site.