How to annotate an image?

Improve the quality of your annotations with our detailed guide on the annotation process in the IKOSA Platform.

Do you need to annotate your images? To help you successfully perform this task, we have prepared this overview for you to make you familiar with the different annotation tools and techniques in IKOSA.

Please note: to be able to annotate the images, you need a previously created project and uploaded some images to it.

What to expect from this page?

Create label sets and labels

Create a new label set

Before you start annotating, you need to define which labels your annotations should be assigned to.

To define a new label set:

  1. Choose the “Label Sets“ page from the left-hand menu.

  2. Click the “Create a new label set“ button

  3. Name your label set and add a description, if necessary, so that you and/or your team members can better understand the purpose of this label (when you later revisit it).

Creating a new label set

Create a label

In the next window, you can add a new label by clicking the “Create new label” button on the bottom left.

Adding labels to a label set

Now you can add:

  • the label name,

  • color and

  • optionally an additional description to the label.

Repeat these steps for all the labels you need for your annotation.

Useful feature: quick label assignment

There are 2 ways to assign labels to annotations:

  • select the special function "Draw and Assign", which allows you to select a label before drawing and automatically assign it to all annotations to be drawn.

  • first, draw all/specific annotations and then assign labels to them.

We recommend using the "Draw and Assign" function, as it enables you to assign labels much faster.

Draw and Assign

If multiple features of the same label are visible and you would like to automatically assign them after drawing, you can choose “Draw and assign“ in the left-hand menu.

Please note: the option to “Draw and assign” is only active, when an appropriate annotation drawing tool has been selected from the right-hand menu.

When the “Draw and assign” option is activated, you can immediately choose one of the labels.

By using this option existing annotations are automatically assigned to the chosen label.

Annotation and label toolset

See for yourself how quickly and conveniently researchers from the Ludwig Boltzmann Institute, Experimental and Clinical Traumatology annotate axons in histological sections of peripheral nerves.

Draw annotation shapes

To start annotating, at first, you need to open an image in your project's image viewer:

  1. Choose the “Image Library” page from the left-hand menu.

  2. Select one of your uploaded images. This leads you to a window with the “Image Viewer”.

On the right-hand side, you will find a toolbar with several tools for drawing annotations. On top of those icons is the annotation/ROI selector. To draw annotations, make sure the slider is on the left side (which is the default).

The rest of the icons represent the following drawing tools:

  • Add “Point” annotation

  • Draw “Rectangle” annotation

  • Draw “Polygon” annotation

  • Draw “Circle” annotation

  • DrawFreeform” annotation

After selecting one of the icons, you can draw the annotation shapes around the given objects within your image by simply using your mouse.

If the first attempt at annotating an object is not perfect, you can modify the shapes within their outlines:

  1. Click the “Edit“ tool in the upper part of the right-hand menu.

  2. Select a given annotation path - its editable anchor points appear as white squares.

  3. Click and drag the anchor points to adjust the shape and fit it to the annotated object.

Delete an existing annotation

Option 1:

  1. Select the annotation you wish to be removed.

  2. Click the “Trash-bin” tool in the upper part of the right-hand menu. You will be asked to confirm this action.

  3. Option 2:

    1. Click the “Trash-bin” tool in the upper part of the right-hand menu.

    2. Click an annotation you wish to be removed. You will be asked to confirm this action.

Assign a label to an existing annotation

To assign a label to an existing annotation:

  1. Choose the “Selection” tool in the upper part of the right-hand menu.

  2. Select an existing annotation by clicking it. Its outlines will appear in bold when selected. Furthermore, the labels in the left-hand menu appear as unchecked.

  3. Click the checkbox next to the selected label to assign this label to a particular annotation. If done correctly, the checkbox will now be active and the annotation will be displayed in the label color.

Now that you have learned how to draw perfect annotations in IKOSA, it is time to embark on exciting image analysis tasks!

Explore all the versatile analysis features IKOSA has to offer!

If you have any questions, please send us an email at (copy-paste your training ID in your email if the question is related to your training).

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