Re: Batch processing of .oib

Posted by Sam Albers on Mar 03, 2010; 9:38pm
URL: http://imagej.273.s1.nabble.com/Re-Batch-processing-of-oib-tp3685528p3685529.html

Hi Curtis,

Thanks for the response.

Your instructions make perfect sense. However, I am stalled by not actually
being able to get the LOCI plugin to do what I want. I would like to be able
to create a TIFF file that is exactly like the one produced when I export a
file from the Olympus viewer (File -> Export, file type=TIFF, output
format=RGB(using assigned LUT), and the "Merge Channel(Amount method)" box
checked).


I recorded the following macros in attempt to produce this same TIFF image
as above using LOCI in Image J. Any thoughts on how I might be able to use
LOCI to do the same as the Olympus software?

run("Bio-Formats Importer", "open=K:\\Confocal_test\\lectinsytoauto.oib
autoscale merge_channels display_metadata view=[Standard ImageJ]
stack_order=Default");
saveAs("Tiff", "K:\\Confocal_test\\lectinsytoauto.tif");

Thanks in advance.


Sam