Re: Min/max constrast values are lost when resampling virtual stacks

Posted by Stein Rørvik on Feb 16, 2017; 11:13pm
URL: http://imagej.273.s1.nabble.com/Min-max-constrast-values-are-lost-when-resampling-virtual-stacks-tp5018115p5018121.html

Thank you for the quick fix!

Stein

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Wayne Rasband
Sent: 16. februar 2017 20:32
To: [hidden email]
Subject: Re: Min/max constrast values are lost when resampling virtual stacks

On Feb 16, 2017, at 7:33 AM, Stein Rørvik <[hidden email]> wrote:
>
> 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.

Thanks to the very helpful test macro, this bug is fixed in the latest ImageJ daily build (1.51k10).

-wayne

> It does not occur with real stacks. 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
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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