Re: Opening Stack with ImageJ and BioFormats

Posted by Wayne Rasband-2 on Oct 29, 2019; 3:39pm
URL: http://imagej.273.s1.nabble.com/Opening-Stack-with-ImageJ-and-BioFormats-tp5022585p5022611.html

> On Oct 28, 2019, at 5:19 AM, Herbie <[hidden email]> wrote:
>
> Dear experts,
>
> a current discussion here on the ImageJ-list leads me to post a question about opening stacks either with "Plain ImageJ" or by using "Bio-Formats Importer" from plain ImageJ.

This bug is fixed in the latest ImageJ daily build (1.52s1). The “Stack to Images” command no longer uses the slice label as the file name if it contains a forward slash or space.

-wayne

> Attached please find a test-stack consisting of two color channels.
>
> 1. "Plain ImageJ"
> (Copy the following macro code lines to an empty macro window
> "Plugins >> New >> Macro" and run it.)
> /////
> open(""); // please open the test-stack
> run("Stack to Images");
> /////
> I get two images with titles:
> "confocal-series_2Ch-0001"
> "confocal-series_2Ch-0002"
>
> 2. "Bio-Formats Importer" from plain ImageJ
> (Copy the following macro code lines to an empty macro window
> "Plugins >> New >> Macro" and run it.)
> /////
> f=File.openDialog(""); // please open the test-stack
> run("Bio-Formats Importer", "open="+f+" color_mode=Default rois_import=[ROI manager] view=[Standard ImageJ] stack_order=Default");
> run("Stack to Images");
> /////
> (Please take care of possible line breaks introduced by the mailer.)
> I get two images with titles:
> "c:1/2 - confocal-series_2Ch"
> "c:2/2 - confocal-series_2Ch"
>
>
> The latter images appear in the Mac-Finder, when saved as TIF, with file names:
> "c/1/2 - confocal-series_2Ch.tif"
> "c/2/2 - confocal-series_2Ch.tif"
>
> For magic reasons the latter image files are correctly opened on my Mac by using the macro:
> (Copy the following macro code lines to an empty macro window
> "Plugins >> New >> Macro" and run it.)
> /////
> f=File.openDialog(""); // please open one of the result images
> open(f);
> /////
> I get the images opened by plain ImageJ with titles:
> "c:1:2 - confocal-series_2Ch.tif"
> "c:2:2 - confocal-series_2Ch.tif"
>
> This may be judged as being nice but I judge it highly confusing.
> From my point of view the prefix introduced by "Bio-Formats Importer" appears being far from reasonable.
>
> Thanks for reading and testing!

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