Question concerning fluorescence intensity

[Yukie Yamahashi]

  Hello. I am trying to quantify stress fiber formation by using Image J.
Could anyone tell me how to measure average fluorescence intensity per cell?
Do I need to define ROI? I just started using Image J, so it would helpful
if you could give me a detailed directions. Thank you.

 Yukie Yamahashi ( a graduate student at Hokkaido Univ., Japan )

[Joachim Wesner]

Hi Yukie,

I fear you won´t get too much help on such a general question about
detailed
instructions for newbies, there is quite a number of IJ "manuals" on the
net to get you into IJ.

The idea is that you really understand whar you are doing, not only follow
a list of
instructions (We also do not know enough about your special problem!!)


Mit freundlichen Grüßen / Best regards

Joachim Wesner
Projektleiter Optik Technologiesysteme

____________________________________________

Leica Microsystems CMS GmbH | GmbH mit Sitz in Wetzlar | Amtsgericht
Wetzlar  HRB 2432
Geschäftsführer:  Dr. Stefan Traeger | Dr. Wolf-Otto Reuter | Dr. David Roy
Martyr | Colin Davis
www.leica-microsystems.com



                                                                           
             Yukie Yamahashi                                              
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             GOV>                       Question concerning fluorescence  
                                        intensity                          
                                                                           
             24.07.2009 13:45                                              
                                                                           
                                                                           
              Bitte antworten                                              
                    an                                                    
              ImageJ Interest                                              
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  Hello. I am trying to quantify stress fiber formation by using Image J.
Could anyone tell me how to measure average fluorescence intensity per
cell?
Do I need to define ROI? I just started using Image J, so it would helpful
if you could give me a detailed directions. Thank you.

 Yukie Yamahashi ( a graduate student at Hokkaido Univ., Japan )



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[ctrueden]

Hi Yukie,

Check out the MBF ImageJ manual:
http://www.macbiophotonics.ca/imagej/

There is also a wiki that has a few things:
http://imagejdocu.tudor.lu/doku.php

And of course the ImageJ web site itself has a lot of good links:
http://rsb.info.nih.gov/ij/docs/index.html

-Curtis

On Sat, Jul 25, 2009 at 2:50 AM, Joachim Wesner <
[hidden email]> wrote:

> Hi Yukie,
>
> I fear you won´t get too much help on such a general question about
> detailed
> instructions for newbies, there is quite a number of IJ "manuals" on the
> net to get you into IJ.
>
> The idea is that you really understand whar you are doing, not only follow
> a list of
> instructions (We also do not know enough about your special problem!!)
>
>
> Mit freundlichen Grüßen / Best regards
>
> Joachim Wesner
> Projektleiter Optik Technologiesysteme
>
> ____________________________________________
>
> Leica Microsystems CMS GmbH | GmbH mit Sitz in Wetzlar | Amtsgericht
> Wetzlar  HRB 2432
> Geschäftsführer:  Dr. Stefan Traeger | Dr. Wolf-Otto Reuter | Dr. David Roy
> Martyr | Colin Davis
> www.leica-microsystems.com
>
>
>
>
>             Yukie Yamahashi
>             <[hidden email]
>             KUDAI.AC.JP>                                               An
>             Gesendet von:              [hidden email]
>             ImageJ Interest                                         Kopie
>             Group
>             <[hidden email].                                       Thema
>             GOV>                       Question concerning fluorescence
>                                        intensity
>
>             24.07.2009 13:45
>
>
>              Bitte antworten
>                    an
>              ImageJ Interest
>                   Group
>             <[hidden email].
>                   GOV>
>
>
>
>
>
>
>  Hello. I am trying to quantify stress fiber formation by using Image J.
> Could anyone tell me how to measure average fluorescence intensity per
> cell?
> Do I need to define ROI? I just started using Image J, so it would helpful
> if you could give me a detailed directions. Thank you.
>
>  Yukie Yamahashi ( a graduate student at Hokkaido Univ., Japan )
>
>
>
> ______________________________________________________________________
> This email has been scanned by the MessageLabs Email Security System.
> For more information please visit http://www.messagelabs.com/email
> ______________________________________________________________________
>

[artgav]

Yukie Yamahashi wrote

  Hello. I am trying to quantify stress fiber formation by using Image J.
Could anyone tell me how to measure average fluorescence intensity per cell?
Do I need to define ROI? I just started using Image J, so it would helpful
if you could give me a detailed directions. Thank you.

 Yukie Yamahashi ( a graduate student at Hokkaido Univ., Japan )

1) Select all cells as described here :
http://naranja.umh.es/~atg/tutorials/VGIV-MeasuringCellsImageJ.pdf  (page 4)
2) Analyze->Set Measurement ( Select Mean &| Median &| Display Label )
3) Select Original picture
4) ROI Manager->Deselect
4) ROI Manager->More->Combine ( all cells will have yellow borders now )
5) Analyze->Measure


You can also use the following macros :

img = getTitle();
setAutoThreshold("Moments dark");
run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 show=Outlines summarize add");
img2 = getTitle();
roiManager("Deselect");
roiManager("Combine");
run("Set Measurements...", "area mean standard modal median display redirect=None decimal=0");
selectImage(img);
roiManager("Combine");
run("Measure");
//roiManager("Delete");
//selectImage(img);
//close();
//selectImage(img2);
//close();

[Nikolaos Kakouros]

Hi Yukie,

I think I'm just trying to do just the same thing now.. Ie I have a photo of fluorescent cells and I wish to measure average intensity per cell.
Did you ever figure out how to do it?
Thanks

Nikos