Batch opening Volocity files

Posted by Marina Franck on Feb 13, 2015; 2:38pm
URL: http://imagej.273.s1.nabble.com/Batch-opening-Volocity-files-tp5011589.html

Hi,

I'm trying to make a macro for batch processing images taken with Volocity. But I stumbled on the first step - I can't get the macro to open the files! Other imaging software save a bunch of files in a folder and I can direct the macro there, but Volocity creates a .mvd2 file and a separate folder containing the data. I can manually open the files in imageJ using the Bio-Formats Importer and asking it to open the .mvd2 file, but the problem is to get this into a macro.

Usually I would start the macro something like this:

dir=getDirectory("Choose Source Directory");
savedir=getDirectory("Choose a Storage Directory");
list = getFileList(dir);
setBatchMode(true)

for (i=0; i<list.length; i++) {
inputPath = dir + list[i];
if (endsWith(inputPath, ".mvd2")) {
                             run("Bio-Formats Importer", "open=[inputPath autoscale color_mode=Grayscale view=Hyperstack stack_order=XYCZT");


...but I think I might need a completely different approach with the Volocity files since it's not a list of .mvd2 files. Any ideas would be appreciated!

Thanks,
Marina
_________________________________________________________________________
Marina Franck, PhD
Department of Neuroscience
Uppsala University
BMC, Box 593, Husargatan 3
751 23  Uppsala
Sweden


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