Average value in summarize table?

[Oliver Dick]

Dear ImageJ users,

I woul like to analyse cell nuclei in a timeseries. I am interested in
the average value of all cells at every given timepoints.
When I use the analyse particle /sumarize function I only can get the
average size. Is there a way to get also the average intensity of the
measured particles?

Thanks in advance for all answers

Oliver

--
Dr. Oliver Dick
Neurobiologie
Im Neuenheimer Feld 364
69120 Heidelberg

Tel.: ++49/(0)6221/548329
Fax.: ++49/(0)6221/546700
Email.: [hidden email]

[Reinhard Mayr aka Czerwinski]

Oliver,

within the Results window, use menu item Edit/Set Measurements to select your desired measurements.

hth,

Reinhard.

-------- Original-Nachricht --------
> Datum: Wed, 10 Sep 2008 14:19:54 +0200
> Von: Oliver Dick <[hidden email]>
> An: [hidden email]
> Betreff: Average value in summarize table?

> Dear ImageJ users,
>
> I woul like to analyse cell nuclei in a timeseries. I am interested in
> the average value of all cells at every given timepoints.
> When I use the analyse particle /sumarize function I only can get the
> average size. Is there a way to get also the average intensity of the
> measured particles?
>
> Thanks in advance for all answers
>
> Oliver
>
> --
> Dr. Oliver Dick
> Neurobiologie
> Im Neuenheimer Feld 364
> 69120 Heidelberg
>
> Tel.: ++49/(0)6221/548329
> Fax.: ++49/(0)6221/546700
> Email.: [hidden email]

--
Psssst! Schon das coole Video vom GMX MultiMessenger gesehen?
Der Eine für Alle: http://www.gmx.net/de/go/messenger03

[GCH-2]

Hi,

You can also use the binarized nuclei as masks and measure the  
average grey values within each nucleus.

Use the following macro as an example:

run("Blobs (25K)");
run("Duplicate...", "title=blobs-1.gif");
run("Make Binary");
run("Set Measurements...", "area mean standard min integrated median  
limit redirect=blobs.gif decimal=2");
run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00  
show=Nothing display exclude");

Gary.
http://www.gcsca.net

On Sep 10, 2008, at 3:47 PM, Reinhard Mayr aka Czerwinski wrote:

> Oliver,
>
> within the Results window, use menu item Edit/Set Measurements to  
> select your desired measurements.
>
> hth,
>
> Reinhard.
>
> -------- Original-Nachricht --------
>> Datum: Wed, 10 Sep 2008 14:19:54 +0200
>> Von: Oliver Dick <[hidden email]>
>> An: [hidden email]
>> Betreff: Average value in summarize table?
>
>> Dear ImageJ users,
>>
>> I woul like to analyse cell nuclei in a timeseries. I am  
>> interested in
>> the average value of all cells at every given timepoints.
>> When I use the analyse particle /sumarize function I only can get the
>> average size. Is there a way to get also the average intensity of the
>> measured particles?
>>
>> Thanks in advance for all answers
>>
>> Oliver
>>
>> --
>> Dr. Oliver Dick
>> Neurobiologie
>> Im Neuenheimer Feld 364
>> 69120 Heidelberg
>>
>> Tel.: ++49/(0)6221/548329
>> Fax.: ++49/(0)6221/546700
>> Email.: [hidden email]
>
> --
> Psssst! Schon das coole Video vom GMX MultiMessenger gesehen?
> Der Eine für Alle: http://www.gmx.net/de/go/messenger03

[Arne Seitz-2]

The Particle Analyser is only working with binarized images therefore the
summary window does not contain average values.

If you want to obtain average pixel values you can either use your binarized
image as mask or add the objects to the ROIManager and measure them on the
original image.

Cheers Arne

____________________________________________________
 
Dr. Arne Seitz, Scientific Officer
Advanced Light Microscopy Facility
EMBL Heidelberg
 
[phone]

-----Ursprüngliche Nachricht-----
Von: ImageJ Interest Group [mailto:[hidden email]] Im Auftrag von
Oliver Dick
Gesendet: Mittwoch, 10. September 2008 14:20
An: [hidden email]
Betreff: Average value in summarize table?

Dear ImageJ users,

I woul like to analyse cell nuclei in a timeseries. I am interested in
the average value of all cells at every given timepoints.
When I use the analyse particle /sumarize function I only can get the
average size. Is there a way to get also the average intensity of the
measured particles?

Thanks in advance for all answers

Oliver

--
Dr. Oliver Dick
Neurobiologie
Im Neuenheimer Feld 364
69120 Heidelberg

Tel.: ++49/(0)6221/548329
Fax.: ++49/(0)6221/546700
Email.: [hidden email]

[Wayne Rasband]

On Sep 10, 2008, at 8:19 AM, Oliver Dick wrote:

> Dear ImageJ users,
>
> I woul like to analyse cell nuclei in a timeseries. I am interested in
> the average value of all cells at every given timepoints.
> When I use the analyse particle /sumarize function I only can get the
> average size. Is there a way to get also the average intensity of the
> measured particles?

In the 1.41l daily build, the Particle Analyzer's "Summarize" option
displays the average particle intensity if "Mean" is enabled in the
Analyze>Set Measurements dialog box. It also displays the average mode,
perimeter, major axis, minor axis, angle, circularity, Feret diameter,
integrated density, median, skewness and kurtosis when these items are
enabled in the Set Measurements dialog.

-wayne