Created attachment 111
simple macros for testing ImageJ2 with QuickPALM plug-in on the cluster

The resulting images after processing them with ImageJ2 together with QuickPalm plugin is not the same as images processed with ImageJ together with QuickPalm. Generally, I have small macros (see attachment) which takes a multi-framed image, splits the channels and then analyses each channel separately with the quickPALM plugin. After analysis and reconstruction I save the resulting images.

I have run this macros both on ImageJ-win64 version of the ImageJ2 (beta version), and the same macros on ImageJ-linux64 (also beta version). The resulting images after reconstruction are different while I would expect them to be identical. 

Also ImageJ-linux64 gives me a warning in the command line: "multichannel image is required". While ImageJ-win64.exe version of ImageJ2 does not complain and have the same results as ImageJ1 version.