How to know what is the unit of area measured in ROI measure? and is there anyway to show the fitted ellipse done by choosing 'ellipse' in 'analyze>set measurement'?

How to know what is the unit of area measured in ROI measure? and is there anyway to show the fitted ellipse done by choosing ‘ellipse’ in ‘analyze>set measurement’?
and what is the degree of angle? (attached) and I dont have idea what is this angle? angle of what? angle of long axis of fitted ellipse? angle of long axis of fitted ellipse with the reference of what?

if your images are not spatially calibrated, then your area typically appears as square pixels (px^2). Otherwise, they appear as the square units at the top left of your image window that tells you your image size. .

Not so sure what you mean by your second question, but if you mean that you want to show the ROIs on your image, I recommend using the ROI manager. Whenever you make a selection, press ‘T’ and if will add that ROI to a list in the ‘ROI manager’, which you can save and recall later. On the ROI manager window, you have the option to ‘Show All’ ROIs that you have selected.

Let me know if that answers some of your questions.

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Thanks so much for quick response. What you mean by " they appear as the square units at the top left of your image window that tells you your image size"? Yes I used set scale.
I chose the ROI to fit ellipse to the image. Now I want to see the fitted ellipse on my image. How can I do that?
Also what is the angle (look at the result table attached to the question). angle of what? what is the unit of angle?

image
Whatever the units are on your image are what your measurements will be outputted as. If there is no scale set, this area will be px^2, and lengths will be px. if 1px = 5 microns and you set that on the ‘Set Scale’ window - as shown below:

image

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@Wilson_Adams Thanks so much. Any idea for the next question?

generally, i think angle will be reported as the angle of a line relative to the horizontal axis of your image in degrees

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@Wilson_Adams I am not sure. Since I fitted an ellipse in to the image, this angle might be related to the fitted ellipse. Is there anyway to see the fitted ellipse?

if you made the ROI in FIJI/ImageJ, then you could use the ROI manager by pressing the t button. but if you made the ROIs in another program, i’m not entirely sure how to import that.

you can do an elliptical selection in FIJI by right-clicking on the circular selection tool. The press ‘t’ to add this to the ROI manager and be able to visualize it on your image. image

Unfortunately, I’m not familiar with an easy way to import ellipses into FIJI based on those measurements.

Maybe you could try converting the dimensions you have into a format that can be read by the ‘makeEllipse()’ macro function?

from Built-in Macro Functions:

makeEllipse(x1, y1, x2, y2, aspectRatio)
Creates an elliptical selection, where x1,y1,x2,y2 specify the major axis of the ellipse and aspectRatio (<=1.0) is the ratio of the lengths of minor and major axis.

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@Wilson_Adams Thanks but I dont want to make ellipse.
Please look at the attached:


“fit ellipse” is selected. I selected this because I am working with a plugin that asks me do to so.
The question I have is what is the reported angle in the result table? and is it related to fitted ellipse?

OH! i see. sorry about that.

my guess is that the if you were to draw a straight line between the major axes of the ellipse, the angle of that line relative to the horizontal axis of the image is what is reported as angle in degrees.

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@Wilson_Adams Makes sense. Is there any way to make sure?

from ImageJ User Guide: https://imagej.nih.gov/ij/docs/guide/146-30.html#sub:Set-Measurements

Fit ellipse Fits an ellipse to the selection. Uses the headings Major , Minor and Angle . Major and Minor are the primary and secondary axis of the best fitting ellipse. Angle is the angle between the primary axis and a line parallel to the X-axis of the image. The coordinates of the center of the ellipse are displayed as X and Y if Centroid is checked. Note that ImageJ cannot calculate the major and minor axis lengths if Pixel Aspect Ratio in the Analyze▷Set Scale…↓ dialog is not 1.0. There are several ways to view the fitted ellipse:

    1. The Edit▷Selection▷Fit Ellipse↑ command replaces an area selection with the best fit ellipse.
    2. The DrawEllipse macro draws (destructively) the best fit ellipse and the major and minor axis.
    3. Select Ellipses from the Show: drop-down menu in the particle analyzer (Analyze▷Analyze Particles…↑) and it will draw the ellipse for each particle in a separate window.
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so yes, it is the angle of the primary axis relative to the horizontal of the image.

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