You can use this tool to maximize the correlation of two images. This can be useful if you experience a certain shift when switching channels. The program calculates the Pearson Product-Moment coefficient and determines to offset where it reaches its maximum. Especially if features are present with the same intensity in both channels, they tend to be aligned very well.
Download Select x64 (64bit) or x86 (32bit) depending on your architecture
This tool is released under the MIT license. Feel free to copy and redistribute it.
You can access the configuration file via About → Open application folder. Right click the configuration.xml file and open with notepad. The following options are available:
MinY: The minimum offset along the X/Y axis in pixel, default
MaxY: The maximum offset along the X/Y axis in pixel, default
ImageJPath: The absolute path to ImageJ (e.g.
null. If specified: ImageJ will be used to perform an actual shift of the images. It is recommended to not touch anything while ImageJ is working ;)
MaxThreads (x64 only): Determines the maximum amount of worker threads. Default
-1, uses twice the amount of logical cores. Set this to a lower number if the program crashes with a memory warning.