Substack and composite

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Substack and composite

Houssin, Nathalie Samantha Laetitia
Hello,

It might seem a very basic thing to do but I would like some advice on generating a composite from a stack :
I tried to make it like this:

  1.  Open .oir file in FIJI (using Pluging > OlympusViewer>Viewer)
  2.  Select z-section
     *   Image>Stacks>Tools>Make Substack
     *   Enter section number (z-value)
When I do this, an exception message appears :

java.lang.IllegalArgumentException: Channel out of range
                at ij.CompositeImage.setChannelLut(CompositeImage.java:538)
                at ij.plugin.SubHyperstackMaker.makeSubhyperstack(SubHyperstackMaker.java:121)
                at ij.plugin.SubHyperstackMaker.makeSubhyperstack(SubHyperstackMaker.java:60)
                at ij.plugin.SubHyperstackMaker.run(SubHyperstackMaker.java:50)
                at ij.plugin.SubstackMaker.run(SubstackMaker.java:33)
                at ij.IJ.runPlugIn(IJ.java:198)
                at ij.Executer.runCommand(Executer.java:137)
                at ij.Executer.run(Executer.java:66)
                at java.lang.Thread.run(Thread.java:745)

And I can't generate a composite file. Any tip on how to proceed will be welcome

Thank you for your time,

Bests,

Nathalie

Nathalie HOUSSIN

Plageman's Lab
Fry Hall room 350
338 W 10th avenue
Columbus, Ohio 43210
Tel: 614-292-0636


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Re: Substack and composite

Wayne Rasband-2
> On Oct 5, 2018, at 6:57 PM, Houssin, Nathalie Samantha Laetitia <[hidden email]> wrote:
>
> Hello,
>
> It might seem a very basic thing to do but I would like some advice on generating a composite from a stack :
> I tried to make it like this:
>
>  1.  Open .oir file in FIJI (using Pluging > OlympusViewer>Viewer)
>  2.  Select z-section
>     *   Image>Stacks>Tools>Make Substack
>     *   Enter section number (z-value)
> When I do this, an exception message appears :

Please provide a MWE (https://en.wikipedia.org/wiki/Minimal_working_example) that reproduces the problem. The following example macro works as expected.

  newImage("HyperStack","16-bit composite-mode label",256,256,3,100,1);
  run("Make Substack...","channels=1-3 slices=50”);

-wayne

> java.lang.IllegalArgumentException: Channel out of range
>                at ij.CompositeImage.setChannelLut(CompositeImage.java:538)
>                at ij.plugin.SubHyperstackMaker.makeSubhyperstack(SubHyperstackMaker.java:121)
>                at ij.plugin.SubHyperstackMaker.makeSubhyperstack(SubHyperstackMaker.java:60)
>                at ij.plugin.SubHyperstackMaker.run(SubHyperstackMaker.java:50)
>                at ij.plugin.SubstackMaker.run(SubstackMaker.java:33)
>                at ij.IJ.runPlugIn(IJ.java:198)
>                at ij.Executer.runCommand(Executer.java:137)
>                at ij.Executer.run(Executer.java:66)
>                at java.lang.Thread.run(Thread.java:745)
>
> And I can't generate a composite file. Any tip on how to proceed will be welcome
>
> Thank you for your time,
>
> Bests,
>
> Nathalie
>
> Nathalie HOUSSIN

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Re: Substack and composite

Houssin, Nathalie Samantha Laetitia
Here is a link to an .oir file I have tried to make a substack with using FIJI as described in my former message.
https://www.dropbox.com/s/m2ykrwu2dvvbcn4/x60-ctl-sample1-Afadin-A568_pmyo-A488_1z.oir?dl=0
I have tried different .oir files and always get the same exception message.

Thank you for your feedback,

Bests,

Nathalie

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Wayne Rasband
Sent: Saturday, October 06, 2018 12:37 AM
To: [hidden email]
Subject: Re: Substack and composite

> On Oct 5, 2018, at 6:57 PM, Houssin, Nathalie Samantha Laetitia <[hidden email]> wrote:
>
> Hello,
>
> It might seem a very basic thing to do but I would like some advice on generating a composite from a stack :
> I tried to make it like this:
>
>  1.  Open .oir file in FIJI (using Pluging > OlympusViewer>Viewer)  
     2.  Select z-section
>     *   Image>Stacks>Tools>Make Substack
>     *   Enter section number (z-value)
> When I do this, an exception message appears :

Please provide a MWE (https://en.wikipedia.org/wiki/Minimal_working_example) that reproduces the problem. The following example macro works as expected.

  newImage("HyperStack","16-bit composite-mode label",256,256,3,100,1);
  run("Make Substack...","channels=1-3 slices=50”);

-wayne

> java.lang.IllegalArgumentException: Channel out of range
>                at ij.CompositeImage.setChannelLut(CompositeImage.java:538)
>                at ij.plugin.SubHyperstackMaker.makeSubhyperstack(SubHyperstackMaker.java:121)
>                at ij.plugin.SubHyperstackMaker.makeSubhyperstack(SubHyperstackMaker.java:60)
>                at ij.plugin.SubHyperstackMaker.run(SubHyperstackMaker.java:50)
>                at ij.plugin.SubstackMaker.run(SubstackMaker.java:33)
>                at ij.IJ.runPlugIn(IJ.java:198)
>                at ij.Executer.runCommand(Executer.java:137)
>                at ij.Executer.run(Executer.java:66)
>                at java.lang.Thread.run(Thread.java:745)
>
> And I can't generate a composite file. Any tip on how to proceed will
> be welcome
>
> Thank you for your time,
>
> Bests,
>
> Nathalie
>
> Nathalie HOUSSIN

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Re: Substack and composite

Wayne Rasband-2
> On Oct 6, 2018, at 11:49 AM, Houssin, Nathalie Samantha Laetitia <[hidden email]> wrote:
>
> Here is a link to an .oir file I have tried to make a substack with using FIJI as described in my former message.
> https://www.dropbox.com/s/m2ykrwu2dvvbcn4/x60-ctl-sample1-Afadin-A568_pmyo-A488_1z.oir?dl=0
> I have tried different .oir files and always get the same exception message.

Thanks for making the .oir file available. The latest ImageJ daily build (1.52h25) fixes the bug that caused Make Substack to throw an exception when used with hyperstacks opened by the OlympusViewer plugin. You can also work around the bug by opening .oir files using BioFormats or by duplicating the virtual stack opened by OlympusViewer to create an in-memory stack.

-wayne


>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Wayne Rasband
> Sent: Saturday, October 06, 2018 12:37 AM
> To: [hidden email]
> Subject: Re: Substack and composite
>
>> On Oct 5, 2018, at 6:57 PM, Houssin, Nathalie Samantha Laetitia <[hidden email]> wrote:
>>
>> Hello,
>>
>> It might seem a very basic thing to do but I would like some advice on generating a composite from a stack :
>> I tried to make it like this:
>>
>> 1.  Open .oir file in FIJI (using Pluging > OlympusViewer>Viewer)  
>     2.  Select z-section
>>    *   Image>Stacks>Tools>Make Substack
>>    *   Enter section number (z-value)
>> When I do this, an exception message appears :
>
> Please provide a MWE (https://en.wikipedia.org/wiki/Minimal_working_example) that reproduces the problem. The following example macro works as expected.
>
>  newImage("HyperStack","16-bit composite-mode label",256,256,3,100,1);
>  run("Make Substack...","channels=1-3 slices=50”);
>
> -wayne
>
>> java.lang.IllegalArgumentException: Channel out of range
>>               at ij.CompositeImage.setChannelLut(CompositeImage.java:538)
>>               at ij.plugin.SubHyperstackMaker.makeSubhyperstack(SubHyperstackMaker.java:121)
>>               at ij.plugin.SubHyperstackMaker.makeSubhyperstack(SubHyperstackMaker.java:60)
>>               at ij.plugin.SubHyperstackMaker.run(SubHyperstackMaker.java:50)
>>               at ij.plugin.SubstackMaker.run(SubstackMaker.java:33)
>>               at ij.IJ.runPlugIn(IJ.java:198)
>>               at ij.Executer.runCommand(Executer.java:137)
>>               at ij.Executer.run(Executer.java:66)
>>               at java.lang.Thread.run(Thread.java:745)
>>
>> And I can't generate a composite file. Any tip on how to proceed will
>> be welcome
>>
>> Thank you for your time,
>>
>> Bests,
>>
>> Nathalie
>>
>> Nathalie HOUSSIN

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