Re: Help - ROI Manager

[Jacqueline Ross]

Hi Haley,

First, check your scale is correct as others have suggested.

Also, if you want to draw a region around your area of interest (ROI), then you need to use the ROI Manager so that your measurements are restricted to that area. Otherwise, the entire image is measured by default.

Draw your region. Open the ROI Manager (Analyze - Tools - ROI Manager) and click Add.

Then use the Measure button in the ROI Manager. This will measure the area inside the region you have drawn.

You still need to set the measurements under Analyze - Set Measurements. If you are not using a threshold, then make sure that Limit to Threshold is not selected.

Kind regards,

Jacqui
________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of Christian Goosmann [[hidden email]]
Sent: 30 October 2012 21:55
To: [hidden email]
Subject: Re: Help

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

... [show rest of quote]

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

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