stack combiner behaving strangely

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stack combiner behaving strangely

TimFeinstein
Hello,

I have noticed an odd behavior in the Image>Stacks>Tools>CombineŠ command.
 Say that I have several 100x100 ROIs in a large 16 bit 3-channel image
that I want to stitch into a mosaic while discarding the rest of the
image.  I create a 100x100 rectangle, duplicate out a few ROIs and use the
crop command to make the last 100x100 ROI.  As far as I can tell the
duplicated ROIs and the cropped ROI are identical.  Two duplicated ROIs
will combine with no problem but when I try to combine a duplicated ROI
with a cropped ROI it tells me that they are not the same data type.  I am
using the latest Fiji update in OSX 10.10.5.  Can anyone replicate this?

Thanks,


Tim

Timothy Feinstein, Ph.D.
Research Scientist
University of Pittsburgh Department of Developmental Biology

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Re: stack combiner behaving strangely

TimFeinstein
Updating my last message, it appears that none of the 100x100 images
created by the Duplicate command (cmd+shift+D, all 3 channels) are
compatible with each other.  Every pairwise combination leads to an error
message that they are not the same data type.  I cannot see anything about
the images themselves that would make the computer think this.


Tim

Timothy Feinstein, Ph.D.
Research Scientist
University of Pittsburgh Department of Developmental Biology





On 11/30/16, 1:24 PM, "Feinstein, Timothy N" <[hidden email]> wrote:

>Hello,
>
>I have noticed an odd behavior in the Image>Stacks>Tools>CombineŠ command.
> Say that I have several 100x100 ROIs in a large 16 bit 3-channel image
>that I want to stitch into a mosaic while discarding the rest of the
>image.  I create a 100x100 rectangle, duplicate out a few ROIs and use the
>crop command to make the last 100x100 ROI.  As far as I can tell the
>duplicated ROIs and the cropped ROI are identical.  Two duplicated ROIs
>will combine with no problem but when I try to combine a duplicated ROI
>with a cropped ROI it tells me that they are not the same data type.  I am
>using the latest Fiji update in OSX 10.10.5.  Can anyone replicate this?
>
>Thanks,
>
>
>Tim
>
>Timothy Feinstein, Ph.D.
>Research Scientist
>University of Pittsburgh Department of Developmental Biology
>

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Re: stack combiner behaving strangely

Michael Schmid
Hi Tim,

sorry, I can't reproduce this. Try this macro:

run("HeLa Cells (1.3M, 48-bit RGB)");
makeRectangle(59, 66, 114, 114);
run("Duplicate...", "title=dup-1 duplicate");
selectWindow("hela-cells.tif");
makeRectangle(275, 82, 114, 114);
run("Duplicate...", "title=dup-2 duplicate");
selectWindow("hela-cells.tif");
makeRectangle(367, 329, 114, 114);
run("Crop");
run("Combine...", "stack1=hela-cells.tif stack2=dup-1");
run("Combine...", "stack1=[Combined Stacks] stack2=dup-2");
run("Select All");

I also tried all three possibilities which 'axis' to define for the
three stack slices in Image>Properties<: c, z, t; it works for all.

I am using a recent daily build (plain ImageJ, not Fiji):
ImageJ 1.51i7; Java 1.6.0_65 [64-bit]

Michael
________________________________________________________________

On 2016-11-30 19:35, Feinstein, Timothy N wrote:

> Updating my last message, it appears that none of the 100x100 images
> created by the Duplicate command (cmd+shift+D, all 3 channels) are
> compatible with each other.  Every pairwise combination leads to an error
> message that they are not the same data type.  I cannot see anything about
> the images themselves that would make the computer think this.
>
>
> Tim
>
> Timothy Feinstein, Ph.D.
> Research Scientist
> University of Pittsburgh Department of Developmental Biology
>
>
>
>
>
> On 11/30/16, 1:24 PM, "Feinstein, Timothy N" <[hidden email]> wrote:
>
>> Hello,
>>
>> I have noticed an odd behavior in the Image>Stacks>Tools>CombineŠ command.
>> Say that I have several 100x100 ROIs in a large 16 bit 3-channel image
>> that I want to stitch into a mosaic while discarding the rest of the
>> image.  I create a 100x100 rectangle, duplicate out a few ROIs and use the
>> crop command to make the last 100x100 ROI.  As far as I can tell the
>> duplicated ROIs and the cropped ROI are identical.  Two duplicated ROIs
>> will combine with no problem but when I try to combine a duplicated ROI
>> with a cropped ROI it tells me that they are not the same data type.  I am
>> using the latest Fiji update in OSX 10.10.5.  Can anyone replicate this?
>>
>> Thanks,
>>
>>
>> Tim
>>
>> Timothy Feinstein, Ph.D.
>> Research Scientist
>> University of Pittsburgh Department of Developmental Biology
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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