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Color profile for calcium waves

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Syla

Color profile for calcium waves

Hello all !

I am beginning to use ImageJ, and I would like to use it to analyse calcium waves in neurons and astrocytes. I acquire stack of images along time, and I can use a ROI to measure fluorescence intensity and make a graph of this intensity over time. But I would like to represent this profile by a color graph, a bit like the 'Line scanning' of Olympus Fluoview software. Shortly speaking, is there a plugin or macro which permit to draw a ROI (line would be better), to get the pixels intensities under this line, and to plot it over time in a 2D graph ?

It should give somethink like this: X-axis is the line profile, Y-Axis is the time.

http://uppix.net/f/b/7/5414812d435051dd24240b31f8dad.jpg

With the 'Dynamic Profiler' I have the first part of this but I couldn't find how to plot it 'graphically'. 'MultiMeasure' gives only graphs and works with areas (and then gives an average, which is less useful for me).

Thank you !

Ford, Glenn (NIH/NLM/LHC) [C]

ImageJ as a java library?

Hello All,

I am new to ImageJ and interested in integrating ImageJ into a large application dealing with multiple media and data types.

Are there any examples of how I can use ImageJ as an imaging library in my Java application? I am specifically interested in the DICOM and Volume rendering rendering/viewing parts but also want to do standard image types (jpeg, etc) as well.

Any help in pointing me to some tutorials/examples is greatly appreciate.

Thank you in advance,

Glenn Ford
Lockheed Martin MSD Consultant
Communications Engineering Branch
National Library of Medicine, Bld 38A

Guido Lütke Wöstmann

Re: ImageJ as a java library?

Ford, Glenn (NIH/NLM/LHC) [C] schrieb:

> Hello All,
>
> I am new to ImageJ and interested in integrating ImageJ into a large application dealing with multiple media and data types.
>
> Are there any examples of how I can use ImageJ as an imaging library in my Java application? I am specifically interested in the DICOM and Volume rendering rendering/viewing parts but also want to do standard image types (jpeg, etc) as well.
>
> Any help in pointing me to some tutorials/examples is greatly appreciate.
>
> Thank you in advance,
>
> Glenn Ford
> Lockheed Martin MSD Consultant
> Communications Engineering Branch
> National Library of Medicine, Bld 38A

Hello,

just download the Javadoc for ImageJ under:

http://rsb.info.nih.gov/ij/download/docs/api.zip

and use the ImageJ-Classes like every other Java-API.
You may start with the Class "ImagePlus" and its Subclass
"DICOM".

Guido

Ford, Glenn (NIH/NLM/LHC) [C]

Re: ImageJ as a java library?

Thank you Guido,

The API can be a bit daunting at first so was hoping some examples to show the different requirements, such as initialization, etc that may not be obvious from reading JavaDoc which can be a bit obscure.

Glenn

-----Original Message-----
From: Guido Lütke Wöstmann [mailto:[hidden email]]
Sent: Wednesday, April 09, 2008 9:50 AM
To: List IMAGEJ
Subject: Re: ImageJ as a java library?

Ford, Glenn (NIH/NLM/LHC) [C] schrieb:

Sami Badawi-2

Re: ImageJ as a java library?

Hi Glenn,

I am not sure I understood your issue, so let me give 2 answers.

1: If your issue is how to run an ImageJ PlugInFilter with other Java
code without starting a ImageJ program up.

This is how I run unit tests for plugins that I have written in
ImageJ, without starting the GUI. I run them either from Eclipse or
from command line using Maven.

public ByteProcessor runPluginFilterOnImage(String fileName, PlugInFilter
plugInFilter) {
Opener opener = new Opener();
ImagePlus image = opener.openImage(fileName);
ByteProcessor bp = (ByteProcessor) image.getProcessor();
plugInFilter.setup("", image);
plugInFilter.run(bp);
return bp;
}

This works if you have written the PlugInFilter. If you want to use
this method for other people's PluginFilter, what ImageJ is doing is
just have the class loader load the PlugInFilter, but class name. You
can do the same.

You can also use a GUI less branch of ImageJ called headless described here:
http://imagejdocu.tudor.lu/imagej-documentation-wiki/faq/how-do-i-run-imagej-without-a-graphics-environment-headless

2: If you issue is how to combine ImageJ with a lot of different
libraries in a somewhat organized way.

I did that using Maven as a build system, and build all my code into a
jar file. I have a little description of what I did here:
http://www.shapelogic.org/setup.html

-Sami Badawi
http://www.shapelogic.org

On Wed, Apr 9, 2008 at 3:19 PM, Ford, Glenn (NIH/NLM/LHC) [C]
<[hidden email]> wrote:

> Thank you Guido,
>
> The API can be a bit daunting at first so was hoping some examples to show the different requirements, such as initialization, etc that may not be obvious from reading JavaDoc which can be a bit obscure.
>
> Glenn
>
>
>
> -----Original Message-----
> From: Guido Lütke Wöstmann [mailto:[hidden email]]
> Sent: Wednesday, April 09, 2008 9:50 AM
> To: List IMAGEJ
> Subject: Re: ImageJ as a java library?
>
> Ford, Glenn (NIH/NLM/LHC) [C] schrieb:
> > Hello All,
> >
> > I am new to ImageJ and interested in integrating ImageJ into a large application dealing with multiple media and data types.
> >
> > Are there any examples of how I can use ImageJ as an imaging library in my Java application? I am specifically interested in the DICOM and Volume rendering rendering/viewing parts but also want to do standard image types (jpeg, etc) as well.
> >
> > Any help in pointing me to some tutorials/examples is greatly appreciate.
> >
> > Thank you in advance,
> >
> > Glenn Ford
> > Lockheed Martin MSD Consultant
> > Communications Engineering Branch
> > National Library of Medicine, Bld 38A
>
> Hello,
>
> just download the Javadoc for ImageJ under:
>
> http://rsb.info.nih.gov/ij/download/docs/api.zip
>
> and use the ImageJ-Classes like every other Java-API.
> You may start with the Class "ImagePlus" and its Subclass
> "DICOM".
>
> Guido
>

Andreas Jahnen

Re: ImageJ as a java library?

In reply to this post by Ford, Glenn (NIH/NLM/LHC) [C]

Dear Glenn,

you might want to look at our DICOM Viewer based on ImageJ

http://santec.tudor.lu/projects/optimage/dicomtools/

You can launch ImageJ from this Swing Application and all the image
functions are "performed" by ImageJ functions. For the moment the viewer
does not support Volume rendering, but we have look into that a bit
already. Please contact me if you need more information about the
software... .

Andreas

-----------------------------------------------------------------
Andreas Jahnen - Ingenieur de Recherche
[hidden email]
-----------------------------------------------------------------
CRP Henri Tudor - http://santec.tudor.lu
2A, rue Kalchesbrück
L-1852 Luxembourg
-----------------------------------------------------------------

ImageJ Interest Group <[hidden email]> wrote on 09.04.2008 15:21:39:

> Hello All,
>
> I am new to ImageJ and interested in integrating ImageJ into a large
> application dealing with multiple media and data types.
>
> Are there any examples of how I can use ImageJ as an imaging library
> in my Java application? I am specifically interested in the DICOM
> and Volume rendering rendering/viewing parts but also want to do
> standard image types (jpeg, etc) as well.
>
> Any help in pointing me to some tutorials/examples is greatly

appreciate.
>
> Thank you in advance,
>
> Glenn Ford
> Lockheed Martin MSD Consultant
> Communications Engineering Branch
> National Library of Medicine, Bld 38A

Tony Collins-4

Re: Color profile for calcium waves

In reply to this post by Syla

Hi,

If you use the line tool (polyline works as well I think) to draw through the region you want to analyse, then you can use the 'Image>Stacks>Reslice' function to generate your pseudo line scan image.

Then you can colour it with the LUTs found under the menu 'Image>Lookup Tables'.

I think the one you show id the 'fire' LUT.

Regards,

Tony

Tony J. Collins, Ph.D.
McMaster Biophotonics Facility
Dept. Biochemistry and Biomedical Sciences HSC 4H21A
McMaster University, Hamilton, ON, L8N 3Z5
[hidden email] www.macbiophotonics.ca

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Syla
> Sent: April 8, 2008 11:10 PM
> To: [hidden email]
> Subject: Color profile for calcium waves
>
> Hello all !
>
> I am beginning to use ImageJ, and I would like to use it to analyse
> calcium
> waves in neurons and astrocytes. I acquire stack of images along time,
> and I
> can use a ROI to measure fluorescence intensity and make a graph of
> this
> intensity over time. But I would like to represent this profile by a
> color
> graph, a bit like the 'Line scanning' of Olympus Fluoview software.
> Shortly
> speaking, is there a plugin or macro which permit to draw a ROI (line
> would
> be better), to get the pixels intensities under this line, and to plot
> it
> over time in a 2D graph ?
>
> It should give somethink like this: X-axis is the line profile, Y-Axis
> is
> the time.
>
> http://uppix.net/f/b/7/5414812d435051dd24240b31f8dad.jpg
>
> With the 'Dynamic Profiler' I have the first part of this but I
> couldn't
> find how to plot it 'graphically'. 'MultiMeasure' gives only graphs and
> works with areas (and then gives an average, which is less useful for
> me).
>
> Thank you !
> --
> View this message in context: http://www.nabble.com/Color-profile-for-
> calcium-waves-tp16578512p16578512.html
> Sent from the ImageJ mailing list archive at Nabble.com.