Annotating Images

In this post, we’re going to look at how to use Fiji to add annotations to an image. Arrows, asterisks and text are all added in roughly the same way. Here’s how:


I’ve previously covered Scale Bars (a type of annotation) and stressed how adding these types of burnt-in features is usually a bad idea. I still stand by that, but there are some cases where you actually do want the features burnt-in.

If you’re set on embellishing your images. Backup the original data and let’s start simple.

Pointing out the obvious

Arrows are a great intuitive way to highlight an object of interest in an image whether you’re publishing with it, using it for a blog or sending a picture to your boss.

Below is an image of a gold nanoparticle but there appears to be an errant crescent-shaped lobe on the left hand side. What I really want to do is make that more obvious.


The arrow tool, is actually a sub-tool of the straight line and you can get to it by right-clicking on the straight line and selecting Arrow.


You can now draw an arrow as you would a line selection (the arrow head is at the end of the line) by clicking and dragging.


What you have just drawn is not an arrow, but an arrow selection (although RenĂ© Magritte may disagree). You can click anywhere in the image and it disappears, you can also hit ‘T’ to add it to the ROI manager, but it’s not part of the image…yet.

Another thing to note is the arrow colour which is set by the selection colour. This can be changed, along with the size of the arrow by double-clicking on the arrow tool, which will bring up the dialog below:


OK, let’s make the arrow a bit bigger by increasing the width:


Much better. OK, so this is now is the point of no return. We want to burn-in the arrow on the original image.

Doing this (and this works with any selection) is as easy as hitting Ctrl+d, also available at [ Edit > Draw ]. You can then deselect the arrow selection (Ctrl+Shift+a or [ Edit > Select > None ] ).


Oh no! What happened? Our lovely red arrow is now grey.

The astute among you will have noticed that the original image is 8 bit greyscale.


This colourspace can only express 256 greyscale values from black (zero) to white (255) and so there is no way to express colour.

You could perfectly happily set the selection colour to white (or any shade of grey) and draw your arrows, but let’s go back to the original image (you can undo this last step with Ctrl + z or [ Edit > Undo ]) and try this again with one small change.

Before you burn in your selection, convert your image from 8-bit, to RGB by running [ Image > Type > RGB Color ]. In the RGB colourspace we can now represent almost any colour we want, including red, so repeat the process and you should have the red arrow of your dreams.


Note the RGB colourspace in the infobar

Asterisk of Gaul

Now that you have the basics down, we’ll move onto Text. Sometimes it’s helpful to direct the attention of the viewer to a particular spot without an arrow. Perhaps you want to identify something that is not otherwise visible like a nucleus or a particle. For this example, we’re going to label a TEM image:


Remember to make the image RGB first!

Select the Text tool (9th tool on the Fiji ToolBar) then drag a box on your image. The size and shape don’t really matter as they’ll change when you start typing text… which is what you should do next, starting with just an asterisk. Now (just as we did with the line tool) double click on the text tool to get the Options dialog from where you can change the size, font and colour of the selection.


At this point, you can drag the selection around or nudge it with the arrow keys until you’re happy with the positioning. Just like last time, Ctrl+d or [ Edit > Draw ] burns it in with the currently selected colour.


Why Stop There?

Of course you can apply as many annotations and embellishments to an image as you want. Just remember that once they’re burned in and saved, you can’t undo it so always (always, always) keep a copy of your original data! Below are a couple of examples of the sorts of things you can do with annotations.


Labelling photos for training materials or demonstrations. Note the two different styles of arrowhead.


Annotating images that do not need to be later quantified (here to show the success of a bacterial transformation). This was done without RGB conversion as we only need white text.


Labelling schematics with non-SI units. Here a background colour is added to the text box which is also rotated. The ‘arrow’ is a double-ended ‘bar’ type.



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