"intensity" in ParticleTable

[Jimmy-Creupagu]

Hi All,

I'm working with QuickPALM and I'm trying to figure out how everything
works.
From the source (MyFunctions.java) I can understand that the label
"intensity" in the ParticleTable refers to the value of the particle:
is it this value only the "peak" (the maximum) or is it the
"integrated volume" (over the particle pixels) of the particle?

Thank you for any help or hint you can give.

Regards

jimmy

[Ricardo Henriques]

Hi Jimmy,

The 'intensity' is the mean intensity of the particle or in other words - the sum of the pixel values for the particle divided by the area of the particle. Here's the code parts that might interest you:

...

int sSum = 0;

...

for (i=xstart;i<=xend;i++)

for (j=ystart;j<=yend;j++)

{

// grab pixel intensity

s=ip.get(i, j);

// check if pixel intensity is above threshold

if (s>thrsh)

{

...

sSum+=s;

npixels++;

}

}

...

double s_ = sSum/npixels;

...

ptable.addValue("Intensity", s_);

...

Hope this helps...

Cheers,

R

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Ricardo Henriques

PhD Student Gene Expression and Biophysics Unit  

Institute of Molecular Medicine

Faculty of Medicine, University of Lisbon Av. Prof. Egas Moniz 

1649-028 Lisbon, Portugal 

Phone: + 351 217999503, 

Ext: 47318 

Fax: + 351 217999504 

E-mail: rhenr...@fm.ul.pt

~~ Or ~~ 

PhD Student (in collaboration with) Groupe Imagerie et Modélisation
(Computational Imaging & Modeling Group)
Département Biologie Cellulaire et Infections
CNRS URA 2582
Institut Pasteur
25-28 rue du Docteur Roux
75015 Paris, France

Phone: +33 1 40 61 31 70

Ext: 3170

E-mail: rica...@pasteur.fr

[gianmarco zanda]

Thank you Ricardo,

It surely helps.
I was looking at the code but I missed some steps!


Cheers,
J

2010/8/25 Ricardo Henriques <paxc...@gmail.com>

[gianmarco zanda]

Hi Ricardo & all,

I'm still working with your plugin and (maybe) I managed to modify the relevant part.
Now, how do I compile it?
I mean, which environment did you use?
I tried to use the java compiler on my desktop and the compile&run feature of imageJ but with no effect.

Thank you for all the support you can give,

Regards

Jimmy

2010/9/3 gianmarco zanda <jama...@gmail.com>

Hi Ricardo & all,

for my project I need to check (and maybe modify) the centroiding algorithm you are using for quickpalm.
In the supplementary note (from nature methods) you state it is a modified center of mass
Can you please tell me where in the source code it is implemented?
It would be really helpful

Thank You very much

J

2010/8/25 gianmarco zanda <jama...@gmail.com>

[Ricardo Henriques]

Hi Jimmy,

I use the standard java compiler (1.6). If you're in a mac try to use this:

-cp /Applications/ImageJ/ij.jar QuickPALM/*.java
jar cvfM QuickPALM_.jar QuickPALM/*.class QuickPALM/*.txt QuickPALM/plugins.config

the instructions are from http://code.google.com/p/quickpalm/wiki/BuildingQuickPALM

If you're able to compile the plugin, then just move the resulting jar file into your ImageJ plugins folder.

Also, if it works out well, think about contributing the code and I will be more than happy to set you as one of the authors/contributors of quickpalm.

Cheers,

R

 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Ricardo Henriques

Gene Expression and Biophysics Unit  
Institute of Molecular Medicine
Faculty of Medicine, University of Lisbon Av. Prof. Egas Moniz 
1649-028 Lisbon, Portugal 
Phone: + 351 217999503, 
Ext: 47318 
Fax: + 351 217999504 
E-mail: rhenr...@fm.ul.pt
~~ Or ~~ 

Unité de Biochimie Structurale et Cellulaire                          
Département de Biologie Structurale et Chimie
Institut Pasteur                          
25 rue du Docteur Roux                          
75724 Paris Cedex 15       

[gianmarco zanda]

Hi Ricardo,

I feel a little stupid now cause I didn't see this part of the wiki at all!
I'll try the modification and if everything works, I'd be more than happy to contribute to the code!

Thank you

Jimmy

2010/10/28 Ricardo Henriques <paxc...@gmail.com>