hull and circle plugin

[TERA EPA]

Hello,
Using the hull and cirlce plug-in I want to identify black dots that are
highly concentrated/dense as a single unit. Is there a way to run the
program to look for these concentrations of black dots?

While looking for these concentrations of black dots we need to be able
adjust the density parameters to more accurately identify these ROI-s, units
of black dots. I want to be able to differentiate the units that may be
close to each other into different units and not counted as one larger unit.


I've tried using the analyze > analyze particles > outline for this purpose,
however, this procedure doesn't gather the black dot concentrations into one
unit, but rather lots of little units which is useless to us.

The hull and circle plug-in may be a superficial way of quantifying these
concentrations of black dots and I am open to any suggestions. The black
dots' 2D spacial proximity to one another is the valuable part of the image.
Maybe there is a different algorithm that relates the proximity and
concentration of the black dots. If anyone can understand what I am saying,
and has something in mind I'd appreciate learning about it.

Thanks,
Emily Cavaliere

TERA (Terrestrial Ecosystem Research Associates)

[audrey karperien-2]

----- Original Message ----
From: TE
Can you give us a sample image?

----- Original Message ----
From: TERA EPA <[hidden email]>
To: [hidden email]
Sent: Tuesday, August 14, 2007 3:45:28 PM
Subject: hull and circle plugin

Hello,
Using the hull and cirlce plug-in I want to identify black dots that are
highly concentrated/dense as a single unit. Is there a way to run the
program to look for these concentrations of black dots?

While looking for these concentrations of black dots we need to be able
adjust the density parameters to more accurately identify these ROI-s, units
of black dots. I want to be able to differentiate the units that may be
close to each other into different units and not counted as one larger unit.


I've tried using the analyze > analyze particles > outline for this purpose,
however, this procedure doesn't gather the black dot concentrations into one
unit, but rather lots of little units which is useless to us.

The hull and circle plug-in may be a superficial way of quantifying these
concentrations of black dots and I am open to any suggestions. The black
dots' 2D spacial proximity to one another is the valuable part of the image.
Maybe there is a different algorithm that relates the proximity and
concentration of the black dots. If anyone can understand what I am saying,
and has something in mind I'd appreciate learning about it.

Thanks,
Emily Cavaliere

TERA (Terrestrial Ecosystem Research Associates)

[audrey karperien-2]

Thanks for the image you sent offlist; as I mentioned, if possible, send us a link to the images.  

I use the particle analyzer to separate out cells on images with multiple cells, and it can be a very good
way of separating the cells from the background, but it does depend on
the image. You may be able to get the particle analyzer working for your images, if I am understanding what you need.  Have you tried setting the size to around 200 pixels, to catch only the groups you are interested in, then doing intervening code to work on the rois using density and proximity, or are you saying that you already tried that?

Audrey
----- Original Message ----
From: audrey karperien <[hidden email]>
To: [hidden email]
Sent: Tuesday, August 14, 2007 4:15:13 PM
Subject: Re: hull and circle plugin

----- Original Message ----
From: TE
Can you give us a sample image?

----- Original Message ----
From: TERA EPA <[hidden email]>
To: [hidden email]
Sent: Tuesday, August 14, 2007 3:45:28 PM
Subject: hull and circle plugin

Hello,
Using the hull and cirlce plug-in I want to identify black dots that are
highly concentrated/dense as a single unit. Is there a way to run the
program to look for these concentrations of black dots?

While looking for these concentrations of black dots we need to be able
adjust the density parameters to more accurately identify these ROI-s, units
of black dots. I want to be able to differentiate the units that may be
close to each other into different units and not counted as one larger unit.


I've tried using the analyze > analyze particles > outline for this purpose,
however, this procedure doesn't gather the black dot concentrations into one
unit, but rather lots of little units which is useless to us.

The hull and circle plug-in may be a superficial way of quantifying these
concentrations of black dots and I am open to any suggestions. The black
dots' 2D spacial proximity to one another is the valuable part of the image.
Maybe there is a different algorithm that relates the proximity and
concentration of the black dots. If anyone can understand what I am saying,
and has something in mind I'd appreciate learning about it.

Thanks,
Emily Cavaliere

TERA (Terrestrial Ecosystem Research Associates)