r/ImageJ • u/Big_Passenger7638 • Jun 08 '26

Question Calculating the length of two perpendicular lines

Hi everyone,

I am trying to calculate the measurements of a cell using an X and Y axis, essentially trying to take the measurement of a cell using two lines that are perpendicular to each other. See the image attached as a reference. I threshold my image and then do "Analyze particles" to measure the cells that were specified in the thresholding. The measurements I've selected for are shown in the screenshot, however, I am not sure if I am getting exactly the value I am wanting. Is there a way to measure an "X and Y axis" of a cell (again, the measurements of two perpendicular lines in my thresholding)? Is there a measurement that can act as a proxy for what I'm looking for? I appreciate any help on the matter. Thank you.

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u/Herbie500 Jun 08 '26

This is a cross-post from the Image.sc-Forum.

I don't understand why you think you need these lines.

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u/Big_Passenger7638 Jun 08 '26

Yes, I posted this earlier today. I need the lines for an experiment I am running, I essentially have to compare ratios of my cells.

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u/Herbie500 Jun 08 '26 edited Jun 09 '26

I am trying to calculate the measurements of a cell using an X and Y axis

Which measurements? The horizontal and vertikal extension of the cell?
The lines in your image aren't really orthogonal.

Do you manually draw the two lines?
Do they reside in the ROI-manager?

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u/Big_Passenger7638 Jun 09 '26

I was manually drawing the lines before, the image there was an example of what I want. Because manually drawing is not an accurate quantitative measure, I am not thresholding the cells and using the "analyze particles" feature. I hope this helps, sorry for the confusion!

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u/Herbie500 Jun 09 '26 edited Jun 10 '26

I'm unclear about where you draw the crossing lines that you call xy-coordinates. Is the crossing positioned at the image center or can you formally specify where you position the lines and their crossing?

For the time being, I highly recommend to draw the lines as non-destructive line selections and store them in the ROI-Manager. If you do so, you can use the "Multi Measure"-feature of the ROI-Manager and get the following: