Loop the Open Image Sequence as Hyperstack function?
Posted by Christine Labno on Jul 10, 2008; 6:28pm
URL: http://imagej.273.s1.nabble.com/Loop-the-Open-Image-Sequence-as-Hyperstack-function-tp3695614.html
Hello group,
I would like to expand on a question posted by Christophe
Leterrier a couple months ago. I am opening also a group of
files like this:
>> image001_ch01
>> image001_ch02
>> image001_ch03
>> image002_ch01
>> image002_ch02. . .
as a hyperstack with LOCI Bio-Formats, using the "group files
with similar names" method suggested by Curtis, and it works
beautifully.
However, the end user has to choose a file from the stack by
hand each time, so only one group/stack can be processed at a
time. Can I set this up to loop and process every group in a
folder, but without opening every .tif and therefore
processing each group multiple times? In other words, how do
I set the script to choose every _nth_ .TIFF file?
I usually use something like this to loop and process
every tiff in a folder:
for (f=0; f<list.length; f++) { //main files loop
path = dir+list[f];
// showProgress(f, list.length);
if (!endsWith(path,"/") && endsWith(path,"f")) open(path);
//do only .tif files
print(path);
if (nImages>=1) {
I'm sure this has been done before, but everything I have
tried seems incompatible with the LOCI importer. Any
suggestions?
Christine
Christine Labno, Ph.D.
Asst. Technical Director
Light Microscopy Core
University of Chicago
Office of Shared Research Facilities
Abbott 129
(773) 834-9040 (phone)