Hey all! I'm new here and to ImageJ. I work with blueberries, mainly with micropropagation. Our group has a desire to measure the surface area of the plants without removing them from test tubes. I am having trouble with running the thresholding tool and getting ImageJ to recognize what is the plant and what is the background. The test tube creates a unique challenge. Rather than fiddling with a bunch of filters and such, I wouldn't mind just editing by hand. I tried this using both the paintbrush tool and the pencil. However, when I ran the measurement, there was no change in the area. Is it possible to outline by hand and have the ImageJ measure area? Is there a better way? I will include some images to explain.
Hi,
First I would recommend you to change the picture background. The background should be completely white or with more light. The first problem that I had was the lines in the background (too dark). For scale setting, try to include a portion of a ruler. I attached what I did. I just needed to adjust B&C settings. In analyze particles, when it says "show" put outlines.
Let me know if you have more questions or if you already figured this out.
Regards,
The background is white but the plants are in test tubes. This is the challenge but figured out the problem with the paintbrush tool was that I didn't have the setting right in measurements. I don't remember what the name was but I basically needed to click a box telling the program to include also what I drew with the paintbrush.
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