As I mentioned before, I am having trouble with using bioformats importer in a macro program to replace File>Open. With File> Open, the code is open(file1 + list1[i]); with i iterating through the list of files in the directory. With Bioformats Importer, you first have to create text for the file then pass it to the bioformats function:
open1=(file1 + list1[i]); //should print "/home/azmanr/folder/file.tiff"
run("Bio-Formats Importer", "open=["+open1+"] autoscale color_mode=Default rois_import=[ROI manager] split_channels view=Hyperstack stack_order=XYCZT");
But, I keep getting null value for open1 and have not been able to pass any filenames to the Bioformats Importer in the for loop, what am I doing wrong? Is it a syntax issue? Here is a link to the full code: http://forum.imagej.net/t/merge-channels-issue/6285/13?u=azmanr
With the Ome.Tiff files I created using ImageJ, they open correctly with File> Open; however, with Bioformats importer my already created merge images appear in seperate channels in greyscale. File> Import> Image opens the merged images formatted correctly, but has c=3 and the c slider bar is showing; the single channel data opens as greyscale instead of the correct color channel. I am now using Tiff files, but I don't understand why there are descrepencies between tiff and ome.tiff as well as between files created manually in ImageJ or bfconvert. Here is a sample ome.tiff file: