How to use multiple tools on ImageJ at once?

I want to use the multipoint tool to count synapses as well as use the straight line tool to section off areas of the imagestack but every time I use the straight line tool to make a line to separate an area, the line disappears once I click elsewhere with the multipoint tool, I need both to stay put. Any way I can do this?

After you make the straight line, press T to add the line to the ROI manager.

Then, on the ROI manager window that appears, check Show All to keep the line visible.

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Thank you tswayne. I tried this and it worked however when I scroll through the Z-axis, it disappears, anyway I can make it stay throughout the slices?

On the ROI manager, click More >> Options and uncheck Associate “Show All” ROIs with slices. If the box is checked, the ROI is visible on the slice it was drawn on. If unchecked, you should be able to see the ROI on all slices.

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The box was unchecked but I am unable to see the ROI on all slices.

I figured it out

Now I’d like to know how I can save it so the lines can be reopened on the same exact position.

Glad it is working so far!

Do you mean you want to show the lines on another image? You can just click on the other image and then click on the ROI representing the line in the ROI manager.

You can also save ROIs to re-open later. In the ROI Manager, if you click More >> you can find a list of commands (explained here) including Save and Open.


Hello Dianne,

If you’d like to save the ROIs together with the image such that they are available after opening that image again, you can store ROIs as a so-called overlay. In simple terms, an overlay is a collection of ROIs that is more closely connected with an image. They can thus be saved with the image in appropriate formats, e.g. TIFF, and are available again after opening the image.

You can convert entries from the ROI manager to an overlay via Image > Overlay > From ROI Manager and vice versa via Image > Overlay > To ROI Manager. Mind the fact that after storing ROIs are as an overlay, they are still available in the ROI manager. You can then go ahead an remove the ROIs from the ROI manager and you should still be able to see them on the image.

You can find more information on the ROI manager and overlays in the ImageJ user guide.