batch merge with differing channel number

Posted by mnqslbs2 on Jun 11, 2015; 3:42pm
URL: http://imagej.273.s1.nabble.com/batch-merge-with-differing-channel-number-tp5013126.html

Hi,
I have a Macro that takes a folder of .LSM Zeiss confocal stacks with varying numbers of channels (between 2 and 4), opens them using the Bio-Formats Importer spliting the channels and saving them as .nrrd, .tif (16bit) and .tif (8bit) in separate folders.  

What I want is to add to this Macro so that it also takes individual channels in the 8bit-tif folder and merges the channels then saves them in a new folder called merged.

The filenames in the 8bit-tif folder are in this format:
BADS01_experiment1_01.tif
BADS01_experiment1_02.tif
BADS02_experiment1_01.tif
BADS02_experiment1_02.tif
BADS02_experiment1_03.tif
BADS03_experiment1_01.tif
BADS03_experiment1_02.tif
BADS03_experiment1_03.tif
BADS03_experiment1_04.tif

Where BADS01, BADS02 and BADS03 are separate samples and the channels are denoted by the two digits before the .tif.

So I need a macro to merge the channels for BADS01, BADS02 and BADS03.

Can anyone help?

Thanks!