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Downloading Plugins

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Bourg, Fred {FLNA}

Downloading Plugins

How does one go about downloading a plugin directly to the plugin folder?

Right now, I copy and paste the source code into Oracle J Developer to recreate the .java file. There must be a better way?:)

Thanks

Fred

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nmichel

Re: Downloading Plugins

Hello,

Try downloading the plugin file and just copying and pasting it in the
plugin folder

Nick

----- Message from [hidden email] ---------
Date: Fri, 2 Nov 2012 13:09:30 -0500
From: "Bourg, Fred {FLNA}" <[hidden email]>
Reply-To: [hidden email]
Subject: Downloading Plugins
To: [hidden email]

> How does one go about downloading a plugin directly to the plugin folder?
>
> Right now, I copy and paste the source code into Oracle J Developer
> to recreate the .java file. There must be a better way?:)
>
> Thanks
>
> Fred
>
> Restricted - Pepsico Confidential
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

----- End message from [hidden email] -----

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Bourg, Fred {FLNA}

Re: Downloading Plugins

I don't see a download option on the plugin webpage. When I select the download link it sends me to a source code listing that is in html or txt format as opposed to the .java file extension

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-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Nikolaos Michelarakis
Sent: Friday, November 02, 2012 2:11 PM
To: [hidden email]
Subject: Re: Downloading Plugins

Hello,

Try downloading the plugin file and just copying and pasting it in the
plugin folder

Nick

----- Message from [hidden email] ---------
Date: Fri, 2 Nov 2012 13:09:30 -0500
From: "Bourg, Fred {FLNA}" <[hidden email]>
Reply-To: [hidden email]
Subject: Downloading Plugins
To: [hidden email]

----- End message from [hidden email] -----

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Bourg, Fred {FLNA}

Downloading Plugins

In reply to this post by Bourg, Fred {FLNA}

ctrueden

Re: Downloading Plugins

In reply to this post by Bourg, Fred {FLNA}

Hi Fred,

> When I select the download link it sends me to a source code listing that
is
> in html or txt format as opposed to the .java file extension

A Java source file is just a text file. Right-click the link to the Java
file in your browser, Save Link As, and save it to your ImageJ plugins
folder.

Then in ImageJ, use Plugins > "Compile and Run..." to run it the first
time. After you run it once, it will appear in the Plugins menu (though you
may need to use Help > Refresh Menus or restart ImageJ to see it).

Regards,
Curtis

On Fri, Nov 2, 2012 at 2:21 PM, Bourg, Fred {FLNA}
<[hidden email]>wrote:

> I don't see a download option on the plugin webpage. When I select the
> download link it sends me to a source code listing that is in html or txt
> format as opposed to the .java file extension
>
>
> Restricted - Pepsico Confidential
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Nikolaos Michelarakis
> Sent: Friday, November 02, 2012 2:11 PM
> To: [hidden email]
> Subject: Re: Downloading Plugins
>
> Hello,
>
> Try downloading the plugin file and just copying and pasting it in the
> plugin folder
>
> Nick
>
> ----- Message from [hidden email] ---------
> Date: Fri, 2 Nov 2012 13:09:30 -0500
> From: "Bourg, Fred {FLNA}" <[hidden email]>
> Reply-To: [hidden email]
> Subject: Downloading Plugins
> To: [hidden email]
>
>
> > How does one go about downloading a plugin directly to the plugin folder?
> >
> > Right now, I copy and paste the source code into Oracle J Developer
> > to recreate the .java file. There must be a better way?:)
> >
> > Thanks
> >
> > Fred
> >
> > Restricted - Pepsico Confidential
> >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
>
> ----- End message from [hidden email] -----
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Bourg, Fred {FLNA}

Re: Downloading Plugins

I've done what you suggest and get the following exception report

java.lang.NullPointerException
at Color_Space_Converter$ColorSpaceConverter.<init>(Color_Space_Converter.java:79)
at Color_Space_Converter.setup(Color_Space_Converter.java:751)
at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:47)
at ij.IJ.runUserPlugIn(IJ.java:187)
at ij.ImageJ.runUserPlugIn(ImageJ.java:292)
at ij.plugin.PlugInExecuter.run(Compiler.java:264)
at java.lang.Thread.run(Thread.java:619)

I appreciate your insights

Fred

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-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Curtis Rueden
Sent: Friday, November 02, 2012 5:07 PM
To: [hidden email]
Subject: Re: Downloading Plugins

Hi Fred,

> When I select the download link it sends me to a source code listing that
is
> in html or txt format as opposed to the .java file extension

A Java source file is just a text file. Right-click the link to the Java
file in your browser, Save Link As, and save it to your ImageJ plugins
folder.

Then in ImageJ, use Plugins > "Compile and Run..." to run it the first
time. After you run it once, it will appear in the Plugins menu (though you
may need to use Help > Refresh Menus or restart ImageJ to see it).

Regards,
Curtis

On Fri, Nov 2, 2012 at 2:21 PM, Bourg, Fred {FLNA}
<[hidden email]>wrote:

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Rasband, Wayne (NIH/NIMH) [E]

Re: Downloading Plugins

On Nov 5, 2012, at 9:08 AM, Bourg, Fred {FLNA} wrote:

> I've done what you suggest and get the following exception report
>
> java.lang.NullPointerException
> at Color_Space_Converter$ColorSpaceConverter.<init>(Color_Space_Converter.java:79)
> at Color_Space_Converter.setup(Color_Space_Converter.java:751)
> at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:47)
> at ij.IJ.runUserPlugIn(IJ.java:187)
> at ij.ImageJ.runUserPlugIn(ImageJ.java:292)
> at ij.plugin.PlugInExecuter.run(Compiler.java:264)
> at java.lang.Thread.run(Thread.java:619)
>
> I appreciate your insights

There was a bug in Color Space Converter plugin that caused it to throw an exception if no image was open. This bug is fixed in the version now available at

http://imagej.nih.gov/ij/plugins/color-space-converter.html

-wayne
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Bourg, Fred {FLNA}

Re: Downloading Plugins

Thanks

I appreciate your patience in helping me get through this.

Fred

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-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Rasband, Wayne (NIH/NIMH) [E]
Sent: Monday, November 05, 2012 8:52 AM
To: [hidden email]
Subject: Re: Downloading Plugins

On Nov 5, 2012, at 9:08 AM, Bourg, Fred {FLNA} wrote:

Franklin Shaffer-2

overlay two stacks, with one stack semi-transparent

I have two stacks of images and I need to overlay the second stack on the first. The second stack is a binarized version of the first stack, with its white areas identifying regions in the first stack.

I need to overlay the second stack onto the first stack, but with the white areas of the second stack being semi-transparent (say, alpha=50) and the black area invisible (alpha=0).

The Add operation in ImageJ's Image Calculator does this, except the white areas of the second stack are not transparent.

Anyone have any suggestions?

Thank you,
Frank

Senior Research Engineer
USDOE National Energy Technology Laboratory
Computational Science Division
Mail Stop 84-202
626 Cochran's Mill Road
Pittsburgh, PA 15236

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Office: 412-386-5964
Cell: 724-970-7262

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Franklin Shaffer.vcf (466 bytes) Download Attachment

Stephan Saalfeld

Re: overlay two stacks, with one stack semi-transparent

Overlaying white with alpha 50 means: 0.5 * A + 0.5 (if white=1)

So make a copy C of binarized stack B, multiply it by -1.0, add 2.0 to
it, divide it by 2 and multiply it with stack A. Now multiply stack B
by 0.5 and add it to that.

If the intensity range in your stack is between 0 and 255, make them
both 32bit float first and divide by 255. After merging, muultiply by
255 again and make them 8bit gray again.

Best,
Stephan

On Mon, 2012-11-05 at 15:11 -0500, Franklin Shaffer wrote:

> I have two stacks of images and I need to overlay the second stack on the first. The second stack is a binarized version of the first stack, with its white areas identifying regions in the first stack.
>
> I need to overlay the second stack onto the first stack, but with the white areas of the second stack being semi-transparent (say, alpha=50) and the black area invisible (alpha=0).
>
> The Add operation in ImageJ's Image Calculator does this, except the white areas of the second stack are not transparent.
>
> Anyone have any suggestions?
>
> Thank you,
> Frank
>
>
>
> Senior Research Engineer
> USDOE National Energy Technology Laboratory
> Computational Science Division
> Mail Stop 84-202
> 626 Cochran's Mill Road
> Pittsburgh, PA 15236
>
> [hidden email]
> Office: 412-386-5964
> Cell: 724-970-7262
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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