Can I add 2 marker colours to an image, both with consecutive numbering?

I’m working with muscle biopsy images and wish to identify and count muscle fibers, then change the marker colour and count the capillaries.


Red circle with consecutive numbering for muscle fibers (Red circle with a number beside it. The number increasing in value for each new circle)

Blue circle with consecutive numbering for capillaries.

I can’t get the point tool to do more than 1 marker with consecutive numbers. Cell counter will place the same number next to a marker of the same type.

How can this be done?

One very easy way to do this:

Select the multipoint tool in the toolbar.

Select the muscle fiber points. If finished add them to the ROI Manager (press ‘t’ or use the menu action):

Rename the multiple points (one ROI Manager item) to, e.g., ‘Muscle Fibers’. The points will be shown as points with a consecutive numbering by default.

Then do the same with the capillaries.

In the ROI Manager there are several options in the ‘Properties’ action to select the color and the shape of the ROI (multipoints). The label (but for all ROI’s) could be changed, too.

Here an example:

Of course you could also write a macro to create overlays, etc. But maybee this fits your needs.



This is what I was wanting. I found a way to do the consecutive numbering with 2 markers using the point tool and flattening the image, before adding the 2nd lot of consecutive numbers. Image->Overlay->Flatten. BUT, this doesn’t allow me to edit points at a later date.

Can I save the ROI’s image as a JPG. I require the images to be viewed outside of ImageJ?

The ROI’s can be saved with the ROI Manager and if you flatten the image (with Show All selected) you get the image with the drawn ellipses. Or you save the file to a *.tif. Then the ROI’s will be stored in the *.tif.

If you reopen the *.tif in ImageJ you can add the ROI’s (overlays) again to the ROI Manager with the overlay action “To ROI Manager” in the menu Image->Overlay.

Of course the *.tif can be viewed outside but the overlays are only shown in ImageJ distributions.

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