48 / 64 bit Composite Image inside an ImageWindow

[Hoover, Karl]

Hi ImageJ programmers,

I am implementing support for 64 bit color images inside the Micro-manager plugin. I found that the CompositeImage subclass of ImagePlus works just fine; I can build a stack of 3 16 bit slices and then create a 48 bit composite image. If I create a new window with show(), the color image is displayed correctly. However, I have trouble when I attempt to display the image within an existing window. I try calling  ImageWindow setImagePlus with my new CompositeImage (which I can do with reflection) however the image region of my ImageWindow is black. Any ideas how to make the existing window display the image the same way a new window displays it?

Thanks,
Karl Hoover

[ctrueden]

Hi Karl,

Sorry for the delay in reply; I'm glad to hear CompositeImage is working for
you.

I initially ran into similar troubles with CompositeImage when reworking the
Bio-Formats Importer. The solution I found was to set the CompositeImage's
channel LUT objects' min and max fields.

The code ends up looking something like:

final CompositeImage compImage = ...;
> final int cSize = compImage.getNChannels();
> for (int c=0; c<cSize; c++) {
>    LUT lut = compImage.getChannelLut(c + 1);
>    lut.min = cMin[c];
>    lut.max = cMax[c];
> }
>

You can see a more complex example of the complete logic used by the
Bio-Formats Importer at:
http://www.loci.wisc.edu/trac/java/browser/tags/loci-tools-4.2.0/components/loci-plugins/src/loci/plugins/in/Colorizer.java

This includes support for properly autoscaling signed integer data using
ImageJ's straight line calibration hack, and a few other edge cases.

HTH,
Curtis

On Tue, Jun 29, 2010 at 2:38 PM, Hoover, Karl <[hidden email]> wrote:

> Hi ImageJ programmers,
>
> I am implementing support for 64 bit color images inside the Micro-manager
> plugin. I found that the CompositeImage subclass of ImagePlus works just
> fine; I can build a stack of 3 16 bit slices and then create a 48 bit
> composite image. If I create a new window with show(), the color image is
> displayed correctly. However, I have trouble when I attempt to display the
> image within an existing window. I try calling  ImageWindow setImagePlus
> with my new CompositeImage (which I can do with reflection) however the
> image region of my ImageWindow is black. Any ideas how to make the existing
> window display the image the same way a new window displays it?
>
> Thanks,
> Karl Hoover
>

[Sindy Kueh]

 
Hi ImageJ users

I am trying to analyse some puncta on a slice.. Interested in areas / size of each puncta.. Tried using the macros (Damon particle analyser) and was asked to create an ROI for the background. Can anyone tell me how to go about doing this.

Also, when I draw a ROI of interest manually to measure each puncta and click measure... I get a measurement of the area in the result output... But when I use the macro... How do I get the areas that are highlighted?

Hope to get some help...

Thanks

Sindy

[dpoburko]

Hi Sindy,

  Damon here. For the "Damon Particle Analyser" the dialog asking for a
background region is expecting you to draw an roi (i.e. a rectangle, an
oval, freehand) that you think is representative of the background
intensity in your image. Once you have drawn the ROI click OK on the
dialog. The mean intensity and n x standard deviations in pixel values
in this region is used to define the lowest threshold that will be used
in the macro. I hope that helped!!

Cheers,
Damon

On 8/17/2011 5:25 PM, Sindy Kueh wrote:

>
> Hi ImageJ users
>
> I am trying to analyse some puncta on a slice.. Interested in areas / size of each puncta.. Tried using the macros (Damon particle analyser) and was asked to create an ROI for the background. Can anyone tell me how to go about doing this.
>
> Also, when I draw a ROI of interest manually to measure each puncta and click measure... I get a measurement of the area in the result output... But when I use the macro... How do I get the areas that are highlighted?
>
> Hope to get some help...
>
> Thanks
>
> Sindy

[Sindy Kueh]

HI Damon,
Will give that a go... Thanks.
Sindy




-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Damon Poburko
Sent: Thursday, August 18, 2011 2:03 PM
To: [hidden email]
Subject: Re: Particle analyser macro

Hi Sindy,

  Damon here. For the "Damon Particle Analyser" the dialog asking for a background region is expecting you to draw an roi (i.e. a rectangle, an oval, freehand) that you think is representative of the background intensity in your image. Once you have drawn the ROI click OK on the dialog. The mean intensity and n x standard deviations in pixel values in this region is used to define the lowest threshold that will be used in the macro. I hope that helped!!

Cheers,
Damon

On 8/17/2011 5:25 PM, Sindy Kueh wrote:

>
> Hi ImageJ users
>
> I am trying to analyse some puncta on a slice.. Interested in areas / size of each puncta.. Tried using the macros (Damon particle analyser) and was asked to create an ROI for the background. Can anyone tell me how to go about doing this.
>
> Also, when I draw a ROI of interest manually to measure each puncta and click measure... I get a measurement of the area in the result output... But when I use the macro... How do I get the areas that are highlighted?
>
> Hope to get some help...
>
> Thanks
>
> Sindy