How to programmatically apply a lut to an image

[Eddie Iannuccelli]

Hello,
Is it possible to programmatically set a lut, let's say Red, green or Blue,
to a 8 bit Image without using IJ.run("color") because my images are not
visibles during processing.

I would like my plugin to save images with differents lut.

Thanks

----------------------------------------
Eddie Iannuccelli
Laboratoire de génétique cellulaire
INRA - Castanet Tolosan
Tel: [phone] / Fax: [phone]

[Wayne Rasband]

> Hello,
> Is it possible to programmatically set a lut, let's say Red, green
> or Blue, to a 8 bit Image without using IJ.run("color") because my
> images are not visibles during processing.
>
> I would like my plugin to save images with differents lut.

In a macro, you can can apply a LUT to a non-visible image by running
the macro in batch mode. Here is an example:

    setBatchMode(true);
    run("Blobs (25K)");
    run("Fire");
    saveAs("Tiff", "/Users/wayne/blobs.tif");

In a plugin, you can do it by using the
WindowManager.setTempCurrentImage() method:

    ImagePlus img = IJ.openImage("/Users/wayne/blobs.tif");
    WindowManager.setTempCurrentImage(img);
    IJ.run("Fire");
    IJ.saveAs("Tiff", "/Users/wayne/blobs2.tif");

-wayne

[Eddie Iannuccelli]

Thank you very much wayne, it works perfectly !

> -----Message d'origine-----
> De : ImageJ Interest Group [mailto:[hidden email]] De la
> part de Wayne Rasband
> Envoyé : jeudi 27 juillet 2006 18:11
> À : [hidden email]
> Objet : Re: How to programmatically apply a lut to an image
>
> > Hello,
> > Is it possible to programmatically set a lut, let's say
> Red, green or
> > Blue, to a 8 bit Image without using IJ.run("color")
> because my images
> > are not visibles during processing.
> >
> > I would like my plugin to save images with differents lut.
>
> In a macro, you can can apply a LUT to a non-visible image by
> running the macro in batch mode. Here is an example:
>
>     setBatchMode(true);
>     run("Blobs (25K)");
>     run("Fire");
>     saveAs("Tiff", "/Users/wayne/blobs.tif");
>
> In a plugin, you can do it by using the
> WindowManager.setTempCurrentImage() method:
>
>     ImagePlus img = IJ.openImage("/Users/wayne/blobs.tif");
>     WindowManager.setTempCurrentImage(img);
>     IJ.run("Fire");
>     IJ.saveAs("Tiff", "/Users/wayne/blobs2.tif");
>
> -wayne
>

[Henry Barwood]

I have installed the plugins to acquire video from Twain and from Quicktime.
Is there a way to perform ImageJ functions on the live feed, or do you
always have to work from the captured video? For instance, could I specify
an ROI and run a histogram or profile while the video is active?

Henry

Henry Barwood
Associate Professor of Science, Earth Sciences
Department of Math and Physics
MSCX 312G
Troy University
Troy, Alabama
[hidden email]

[Wayne Rasband]

> I have installed the plugins to acquire video from Twain and
> from Quicktime. Is there a way to perform ImageJ functions
> on the live feed, or do you always have to work from the
> captured video? For instance, could I specify an ROI and run
> a histogram or profile while the video is active?

You can create ROIs, generate histograms (press "h") or generate
profile plots (press "k") while the QuickTime Capture plugin
(http://rsb.info.nih.gov/ij/plugins/qt-capture.html) is in "Live" mode.
This plugin is built in as the File>Import>Video command on the Mac
version of ImageJ.

-wayne

[Henry Barwood]

Hi Wayne,

Thanks for the information. I've hit a small snag. The camera I had planned
on using does not function via VDig and Quicktime. I wonder it there is
anyone who has worked with older webcams who might have a workaround to
this. My camera is a 3Com USB that has excellent low-light capabilities and
can capture emission spectra at very low light levels. It works great with
JTwain, but not Quicktime.

Henry

Henry Barwood
Associate Professor of Science, Earth Sciences
Department of Math and Physics
MSCX 312G
Troy University
Troy, Alabama
[hidden email]


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Wayne
Rasband
Sent: Friday, July 28, 2006 11:43 AM
To: [hidden email]
Subject: Re: Live video feed - can you perform functions on?

> I have installed the plugins to acquire video from Twain and
> from Quicktime. Is there a way to perform ImageJ functions
> on the live feed, or do you always have to work from the
> captured video? For instance, could I specify an ROI and run
> a histogram or profile while the video is active?

You can create ROIs, generate histograms (press "h") or generate
profile plots (press "k") while the QuickTime Capture plugin
(http://rsb.info.nih.gov/ij/plugins/qt-capture.html) is in "Live" mode.
This plugin is built in as the File>Import>Video command on the Mac
version of ImageJ.

-wayne

[Vincenzo Della Mea]

If on Windows, did you try the WinVDIG driver suggested on the  
plugins web page?

Vincenzo

Il giorno 28/lug/06, alle ore 20:27, Henry Barwood ha scritto:

> Hi Wayne,
>
> Thanks for the information. I've hit a small snag. The camera I had  
> planned
> on using does not function via VDig and Quicktime. I wonder it  
> there is
> anyone who has worked with older webcams who might have a  
> workaround to
> this. My camera is a 3Com USB that has excellent low-light  
> capabilities and
> can capture emission spectra at very low light levels. It works  
> great with
> JTwain, but not Quicktime.

[Henry Barwood]

Hi,

Yes, I tried WinVDig but it did not recognize the 3Com camera (apparently
only twain drivers exist in this now defunct camera). Thanks.

Henry

Henry Barwood
Associate Professor of Science, Earth Sciences
Department of Math and Physics
MSCX 312G
Troy University
Troy, Alabama
[hidden email]

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Vincenzo Della Mea
Sent: Saturday, July 29, 2006 3:18 AM
To: [hidden email]
Subject: Re: Live video feed - can you perform functions on?

If on Windows, did you try the WinVDIG driver suggested on the  
plugins web page?

Vincenzo

Il giorno 28/lug/06, alle ore 20:27, Henry Barwood ha scritto:

> Hi Wayne,
>
> Thanks for the information. I've hit a small snag. The camera I had  
> planned
> on using does not function via VDig and Quicktime. I wonder it  
> there is
> anyone who has worked with older webcams who might have a  
> workaround to
> this. My camera is a 3Com USB that has excellent low-light  
> capabilities and
> can capture emission spectra at very low light levels. It works  
> great with
> JTwain, but not Quicktime.

[Vincenzo Della Mea]

At this point, you can try a generic WDM driver like btwincap  
(together with WinVDIG).
Vincenzo

Il giorno 30/lug/06, alle ore 22:11, Henry Barwood ha scritto:

> Hi,
>
> Yes, I tried WinVDig but it did not recognize the 3Com camera  
> (apparently
> only twain drivers exist in this now defunct camera). Thanks.
>
> Henry
>
> Henry Barwood
> Associate Professor of Science, Earth Sciences
> Department of Math and Physics
> MSCX 312G
> Troy University
> Troy, Alabama
> [hidden email]
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Vincenzo Della Mea
> Sent: Saturday, July 29, 2006 3:18 AM
> To: [hidden email]
> Subject: Re: Live video feed - can you perform functions on?
>
> If on Windows, did you try the WinVDIG driver suggested on the
> plugins web page?
>
> Vincenzo
>
> Il giorno 28/lug/06, alle ore 20:27, Henry Barwood ha scritto:
>
>> Hi Wayne,
>>
>> Thanks for the information. I've hit a small snag. The camera I had
>> planned
>> on using does not function via VDig and Quicktime. I wonder it
>> there is
>> anyone who has worked with older webcams who might have a
>> workaround to
>> this. My camera is a 3Com USB that has excellent low-light
>> capabilities and
>> can capture emission spectra at very low light levels. It works
>> great with
>> JTwain, but not Quicktime.

* Vincenzo Della Mea
* Medical Informatics, Telemedicine and Ehealth Lab
* University od Udine, Italy
* http://mitel.dimi.uniud.it/  -  http://www.eslide.net

[Joachim Wesner]

Hi forum,

can somebody probably point me to some simple Java example code or working
plugin with such Java code
that implements a simple but NON-MODAL dialog with sliders? The shorter the
example/plugin code the better!

I want to implement some special model fitting plugin and would like to be
able to change parameters with the sliders and
immediatelly see the results.

Thanky you!

Joachim


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[dscho]

Hi,

On Mon, 31 Jul 2006, Joachim Wesner wrote:

> can somebody probably point me to some simple Java example code or
> working plugin with such Java code that implements a simple but
> NON-MODAL dialog with sliders? The shorter the example/plugin code the
> better!

ij.gui.StackWindow ;-)

The scrollbar ("sliceSelector") is the slider.

Hth,
Dscho