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Circumference of a coral lesion

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The lesion is the white spot

This came from an environmental researcher: "I need to determine the circumference of a coral lesion with a metric stick in the same picture." The goal is to "determine how well corals are able to recover from damage or stress".

This is what I was able to do with Pixcavator in about 10 minutes.

First, I cropped the image to speed up processing time. Then I ran the analysis. To capture the lesion I had to move the first slider almost all way to the right. The green contour then appears to capture the lesion well enough - the first screenshot. (The same result can be obtained using the other sliders.) Then in the table on the right you can see the size (area) of the spot: 19516 pixels. If you want to find the diameter, you can treat the spot as a circle with area 19516. Then the diameter is 2*sqrt(area/Pi) = 158.

lesion captured inside green contour, measurements on the right

Now, this result is in pixels. Pixcavator does not have at this time an automatic calibration feature but it can be done nonetheless. Out of many ways to do it - turn pixels into centimeters - I chose just one. In the second screenshot you can see that I captured two lines on the stick. Their second coordinates are 225 and 258. Then we have 5mm = 258 - 225 = 33 pixels. So the diameter is 158/33*5 = 79 mm which is reasonably close to what you see. If the setup is always the same, the calibration part will have to be done only once.

calibration

Run this analysis with Pixcavator SI.

Other image analysis examples