Posted by
Stein Rørvik on
Feb 16, 2017; 12:33pm
URL: http://imagej.273.s1.nabble.com/Min-max-constrast-values-are-lost-when-resampling-virtual-stacks-tp5018115.html
This is a related issue to that described in my last post:
When working with virtual stacks, any min/max constrast values that are set after opening the stack, are lost when rescaling or making a substack. This problem occurs both via then GUI and via macros. It does not occur with real stacks. I assume this is because when working with virtual stacks, if the min/max setting was not already saved in the original files, it is forgotten when the files are re-read from files during the rescale or substack operations.
The reason this (minor) issue is an annoyance for me, is that in my case the virtual stack import is done by a macro that automatically sets the proper min/max values based on material data available in a metafile, so I need to relocate and re-set the proper min/max values whenever I want to scale or make a substack from a virtual stack when using the GUI. In a macro this is not a problem of course, as I then just need to use the getMinAndMax command.
Anyway, the following macro reproduces the problem:
//open sample data, and save as separate images in a folder in order to make a virtual stack
run("T1 Head (2.4M, 16-bits)");
run("Image Sequence... ", "format=TIFF save=C:\\Users\\steinr\\T1-virtual-stack\\");
close();
run("Image Sequence...", "open=C:\\Users\\steinr\\T1-virtual-stack\\ sort use");
setSlice(64);
setMinAndMax(1, 300); //the brightness was increased because we say we are interested in the darker tissue
//extract a substack
selectWindow("T1-virtual-stack");
run("Make Substack...", " slices=60-70");
setSlice(5); //same as original slice 64
//the min/max setting was lost
//resample the stack
selectWindow("T1-virtual-stack");
run("Scale...", "x=.5 y=.5 z=.5 width=128 height=128 depth=64 interpolation=Bilinear average process create title=T1-virtual-stack-16bit-scaled");
setSlice(32);
//the min/max setting was lost
//For comparison: When working with true stacks, the min/max constrast values are kept properly:
run("T1 Head (2.4M, 16-bits)");
setSlice(64);
setMinAndMax(1, 300);
//extract a substack
selectWindow("t1-head.tif");
run("Make Substack...", " slices=60-70");
setSlice(5); //same as original slice 64
//the min/max setting was kept
//resample the stack
selectWindow("t1-head.tif");
run("Scale...", "x=.5 y=.5 z=.5 width=128 height=128 depth=64 interpolation=Bilinear average process create title=T1-virtual-stack-16bit-scaled");
setSlice(32);
//the min/max setting was kept
run("Tile");
Stein
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