Re: Batch processing of .oib
Posted by
Glen MacDonald-2 on
Mar 03, 2010; 11:20pm
URL: http://imagej.273.s1.nabble.com/Re-Batch-processing-of-oib-tp3685528p3685530.html
Dear Sam and Curtis,
With the LOCI plugin, selecting to import Olympus 3-channel OIB or OIF into RGB merge, the result is 16-bit monochrome with interleaved channels. Occurs with 'old' files acquired by Fluoview pre-2.0 and with 2.0c.
The Olympus viewer output for a 2D 3-channel OIB or OIF is a 24-bit color merge.
Sam, the macro I sent to you uses the LOCI plugin to open each channel individually (LOCI 'Split channels'), and uses the ImageJ 'Image/Color/Merge channels..' command to merge the channels in your selected channel order. When you say that the macro doesn't give the save result as the Fluoview Viewer, are you setting the channel order correctly? Lowest channel number is the shortest emission wavelength.
Regards,
Glen
On Mar 3, 2010, at 1:38 PM, Sam Albers wrote: a
Glen MacDonald
Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
Box 357923
University of Washington
Seattle, WA 98195-7923 USA
(206) 616-4156
[hidden email]
> 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