Problem with area measurement

[kevin egan]

Hello again,

I have been having a problem with the Analyze particles tool in Image
J. If the area I am measuring has any fully enclosed white spaces
(after thresholding the image), it measures these areas as being part
of the  black areas. This skews our data as we wish to know the area
calculations for the black areas, not including any fully enclosed
white areas. I knonw this is probably a poor explanation so I made a
picture describing the problem. The picture is at my personal webspace
http://users.drew.edu/kegan/ex.jpg.
 I wish to use the Analyze particles tool to measure the area of the
black space in the picture, but when I measure it with Image J, it is
including these white "void" areas in the measurement. I have tried
limit to threshold, exclude on edges, flood fill, and various other
suggestions that I have found after searching through the archives.
Does the program currently have this functionality or is it in a
plugin that is out there or a plug in that is yet to be written?

Thank you very much for your help.

Kevin Egan

[Gabriel Landini]

On Tuesday 19 July 2005 20:02, kevin egan wrote:
> I have been having a problem with the Analyze particles tool in Image
> J. If the area I am measuring has any fully enclosed white spaces
> (after thresholding the image), it measures these areas as being part
> of the  black areas.

Not sure what the problem is (I am writing this off-line), but if you want to
measure a blob without the holes, you could do:

1. Use the Analyze Particles to get the area of the blob, then invert the
image and measure the area of the holes and subtract this value from the
other.

2. Use one of the plugins Particles4, Particles8, or  Particles8_plus in the
Morphology collection (below). These give you the *number of pixels* of a
blob, taking into accout any holes.
http://www.dentistry.bham.ac.uk/landinig/software/software.html

I hope it helps.

G.

[Laura DiNicola]

are you sure it is counting the holes?  i had a similar problem, and all i did was threshold the image, reselect it by clicking on the black area on the outside with the wand tool, and use the analyze particles tool.  i know this worked because i double checked it by using the measure->area tool and then held alt down while clicking the wand in the white areas.  each time i measured it, the area was smaller, and when i clicked on all of the white areas, i got the same number as i did with the analyze particles tool.  




 --- On Tue 07/19, Gabriel Landini < [hidden email] > wrote:
From: Gabriel Landini [mailto: [hidden email]]
To: [hidden email]
Date: Tue, 19 Jul 2005 22:50:31 +0100
Subject: Re: Problem with area measurement

On Tuesday 19 July 2005 20:02, kevin egan wrote:<br>> I have been having a problem with the Analyze particles tool in Image<br>> J. If the area I am measuring has any fully enclosed white spaces<br>> (after thresholding the image), it measures these areas as being part<br>> of the  black areas. <br><br>Not sure what the problem is (I am writing this off-line), but if you want to <br>measure a blob without the holes, you could do:<br><br>1. Use the Analyze Particles to get the area of the blob, then invert the <br>image and measure the area of the holes and subtract this value from the <br>other.<br><br>2. Use one of the plugins Particles4, Particles8, or  Particles8_plus in the <br>Morphology collection (below). These give you the *number of pixels* of a <br>blob, taking into accout any holes. <br>http://www.dentistry.bham.ac.uk/landinig/software/software.html<br><br>I hope it helps.<br><br>G.<br>

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[Wayne Rasband]

 > I have been having a problem with the Analyze particles tool
 > in ImageJ. If the area I am measuring has any fully enclosed
 > white spaces (after thresholding the image), it measures these
 > areas as being part of the  black areas. This skews our data
 > as we wish to know the area calculations for the black areas,
 > not including any fully enclosed white areas.

There are two ways to exclude interior holes when using the particle
analyzer. One way is to threshold the image and check "Limit to
Threshold" in the Set Measurements dialog. The other way is to check
"Flood Fill" in the Analyze Particles dialog (requires ImageJ 1.34).

-wayne