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Frequency and area analysis

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Nessler, Randy A

Frequency and area analysis

I have some cardiac cell cultures where certain clumps of cells are
beating. The control dish has a different beat frequency than the
experimental and the number of beating clumps (area) differs as well.
Images can be acquired via a CCD camera at 5 frames a second or video
camera with a digitizing board. Is there an automated approach to
answering (quantifying) the different frequency at which they are
beating and also compare the area of beating clumps between the
cultures? I guess the area question could be answered by hand drawing
roi's, but it seems it would be easier if they were selected due to
motion.

Thanks in advance,
Randy Nessler

Pedro Alejandro Herve Fernandez Carrera Licenciatura en Cs.Biologicas

Re: Frequency and area analysis

hi, if the cells are beating or moving (quite impressive), and you are also
taking a stack of pictures (five per second), open the sequence (file/open as
image sequence), then go to edit and invert them (all the pictures will be
black and white), make a copy of the first picture of the stack (by pressing
shift + control + d), now you make a selection of your culture and copy (by
pressing "c"), move it over the cell or cells that beats, and press "v",
after all this go to process/image calculator and substract the copy to the
stack (process all the stack), then go to image/adjust threshold to make your
cells visible, and then i think you can use an area measurer plugin (if you
find it please contact me).
this example i took ot from the moving analisys of two larvae on the web page
of imagej.
sorry about my english.
let me know if it worked.
bye

kiran kumar-3-3

Threshold Adjuster

In reply to this post by Nessler, Randy A

Hello group,

I am writing a plugin for analysis of SEM image and
using threshold adjuster for adjusting the threshold.
I need to give indefinite time to the user to adjust
it and after he clicks the button apply then I have to
proceed with next operations.

But I figured out that i need to use Event listeners
but doesnt know how to get instance of button Apply of
threshold adjuster class.

I would be gratefull if anyone could help me find a
solution.

Thanks,

Regards,
Kiran

__________________________________
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Leon Espinosa

Re: Threshold Adjuster

I know this...
This a plugin that add a listener (save this code as "Threshold_2.java"
compile it with "compile and run"):

import ij.*;
import ij.process.*;
import ij.gui.*;
import ij.plugin.*;
import ij.plugin.frame.*;
import ij.plugin.frame.ThresholdAdjuster.*;

import java.lang.*;
import java.lang.Object.*;
import java.awt.*;
import java.awt.event.*;
import java.awt.event.WindowEvent.*;

public class Threshold_2 implements PlugIn {

int wclose = 202;

public void run(String arg) {
CustomThresholdAdjuster2 seuil = new CustomThresholdAdjuster2();

while(!(seuil.getWclose==wclose)) {}
IJ.showMessage(" la suite...");

}

}

class CustomThresholdAdjuster2 extends ThresholdAdjuster {

public int getWclose;
boolean fin = false;

public void windowClosing(WindowEvent w) {
super.windowClosing(w);
String Waction = w.paramString();
getWclose = w.WINDOW_CLOSED;

}

}

//------------------------------------------------------------ END
-------------------

Now you will have a new "Threshold_2.class" in the plugins folder, close
ImageJ and start again, now you can use it in your macros, exemple:

macro.txt:

showMessage("Set Threshold and close the window to continue");
run("Threshold 2");
getThreshold(lower, upper);

Your code here...

A 11:27 13/10/2005 -0700, KIRAN kumar a écrit :

>Hello group,
>
> I am writing a plugin for analysis of SEM image and
>using threshold adjuster for adjusting the threshold.
>I need to give indefinite time to the user to adjust
>it and after he clicks the button apply then I have to
>proceed with next operations.
>
> But I figured out that i need to use Event listeners
>but doesnt know how to get instance of button Apply of
>threshold adjuster class.
>
> I would be gratefull if anyone could help me find a
>solution.
>
>Thanks,
>
>Regards,
>Kiran
>
>
>
>__________________________________
>Yahoo! Music Unlimited
>Access over 1 million songs. Try it free.
>http://music.yahoo.com/unlimited/

Leon Espinosa
04 91 32 46 25
06 79 25 97 40
Unité des Rickettsies
Fac. de la Timone
27 Bd Jean Moulin
13005 Marseille

Leon Espinosa

Re: Threshold Adjuster

In reply to this post by kiran kumar-3-3

Dear Kiran
This the same plugin but it waits for the "Apply" button (same procedure:
save as Threshold_3.java, compile it and use in your macro with

run("Threshold 2");

//-----------------------------------------------

import ij.*;
import ij.process.*;
import ij.gui.*;
import ij.plugin.*;
import ij.plugin.frame.*;
import ij.plugin.frame.ThresholdAdjuster.*;

import java.lang.*;
import java.lang.Object.*;
import java.awt.*;
import java.awt.event.*;
import java.awt.event.WindowEvent.*;

public class Threshold_3 implements PlugIn {

public void run(String arg) {
CustomThresholdAdjuster3 seuil = new CustomThresholdAdjuster3();
}

}

class CustomThresholdAdjuster3 extends ThresholdAdjuster {

boolean fin = false;

public void actionPerformed(ActionEvent e) {
super.actionPerformed(e);
String action = e.getActionCommand();

if (action=="Apply") {
fin = true;
this.close();
IJ.showMessage(" la suite...");
}

}
}

//-------------- end -----------------------

A 11:27 13/10/2005 -0700, vous avez écrit :

Leon Espinosa
04 91 32 46 25
06 79 25 97 40
Unité des Rickettsies
Fac. de la Timone
27 Bd Jean Moulin
13005 Marseille