Opening Stack with ImageJ and BioFormats

Posted by Herbie on Oct 28, 2019; 9:19am
URL: http://imagej.273.s1.nabble.com/Opening-Stack-with-ImageJ-and-BioFormats-tp5022585.html

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.

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!

Regards

Herbie




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