Help

[Haley Nelson]

I am new to Image J and having trouble with area measurements. I'm interested in measuring the area of the striatum in mice brains that I have stained with H&E. I have many sections and plan to use the Cavalieri method when I have all the area measurements to calculated volume. The area results number is way to high. I have done the following:

1. Convert scanned color image of leaf to grayscale: Image → Type → 8-bit
2. Set measurement scale: highlighted known distance line: Analyze → Set Scale
3. In Set Scale window enter 1000 into the 'Known Distance' box and change the 'Unit of Measurement' box to microns, check 'Global'
4. Draw a new line and confirm that the measurement scale is correct.
5. Draw an outline around the striatum.
6. Measure

In the area column, it is way to high 5.9E6 microns. Is this the right method to measure the area?
 Thanks,
Haley

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[JimmiB]

Hi Haley,

From the sound of it you have set the scale of the image to
1000 microns/pixel.
You need to know the correct scale of your image, which will
be dependent on the objective and image sensor you used.  This
may be embedded in the image already.
Ask someone who works in your facility if they can let you
know the scale.
James

"There's a fine line between fishing and just standing on the
shore like an idiot."
--------------------------------------------------------------
--------
James Burchfield  PhD

Garvan Institute of Medical Research
St Vincents Hospital                 Ph   :   [phone]
384 Victoria St                   O403 977
448
Darlinghurst  NSW 2010
Australia                                 email:  
[hidden email]
http://www.garvan.org.au
--------------------------------------------------------------
--------


---- Original message ----
>Date: Tue, 30 Oct 2012 00:33:49 -0400
>From: ImageJ Interest Group <[hidden email]> (on behalf
of Haley Nelson <[hidden email]>)
>Subject: Help  
>To: <[hidden email]>
>
>I am new to Image J and having trouble with area
measurements. I'm interested in measuring the area of the
striatum in mice brains that I have stained with H&E. I have
many sections and plan to use the Cavalieri method when I have
all the area measurements to calculated volume. The area
results number is way to high. I have done the following:
>
>1. Convert scanned color image of leaf to grayscale: Image →
Type → 8-bit
>2. Set measurement scale: highlighted known distance line:
Analyze → Set Scale
>3. In Set Scale window enter 1000 into the 'Known Distance'
box and change the 'Unit of Measurement' box to microns, check
'Global'
>4. Draw a new line and confirm that the measurement scale is
correct.
>5. Draw an outline around the striatum.
>6. Measure
>
>In the area column, it is way to high 5.9E6 microns. Is this
the right method to measure the area?
> Thanks,
>Haley
>
>--
>ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Christian Goosmann]

---
Christian Goosmann
Mikroskopie
Max-Planck-Institut für Infektionsbiologie
Campus Charité Mitte
Charitéplatz 1
10117 Berlin
Tel.: [phone]

Haley Nelson wrote:

> I am new to Image J and having trouble with area measurements. I'm interested in measuring the area of the striatum in mice brains that I have stained with H&E. I have many sections and plan to use the Cavalieri method when I have all the area measurements to calculated volume. The area results number is way to high. I have done the following:
>
> 1. Convert scanned color image of leaf to grayscale: Image → Type → 8-bit
> 2. Set measurement scale: highlighted known distance line: Analyze → Set Scale
> 3. In Set Scale window enter 1000 into the 'Known Distance' box and change the 'Unit of Measurement' box to microns, check 'Global'
> 4. Draw a new line and confirm that the measurement scale is correct.
> 5. Draw an outline around the striatum.
> 6. Measure
>
> In the area column, it is way to high 5.9E6 microns. Is this the right method to measure the area?
>   Thanks,
> Haley
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

Hi Haley,
the way you do it sounds correct. So you have some feature in your image
that you know resembles 1mm and you set the scale so it equals 1000µm.
If your outline has an area similar to a square with the side length of
a bit more than twice your mentioned feature ~2.23 mm), your result can
be ~ 5 x 10^6 µm², or ~ 5mm². Or did my maths leave me?
Christian

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html