Day 8 – Annotations with

In our previous episode we started exploring, our integrated slide viewing solution. is a beefed version of PMA.view, which we discussed earlier on in part two of this tutorial series. If you haven’t gone through part two or part 7 of our tutorial series, we highly recommend you do so first. Going forward, we will assume that you already have some familiarity with PMA.view as well as


On-slide annotations are a staple in pathology. supports several ways of creating and managing them.

Access to’s annotation functions is handled via a dedicated tab on the ribbon:

The first thing you probably want to do when working with annotations is to enable to annotations panel:

After clicking on it, your screen should look like this:

Ok, that’s not all that impressive yet. We haven’t made any actual annotation yet, of course. Let’s go ahead and do that. Let’s focus on the basic annotations for the time being. This is the top line of icons in the “Shapes” group on the ribbon tab.

Let’s start by drawing a first circle. Upon completion, you’ll notice that the new annotation automatically is added to the list in the annotations panel:

When you select the annotation on the slide, the corresponding entry in the list is selected as well, and vice versa.

You can use the colorpicker and select the pen width from the first Annotations group on the ribbon tab to change the color and the line thickness if you want to.

Now go ahead and play a bit with the different shapes. Draw some circles, rectangles, arrows, and see how they interact with the annotations panel. Eventually you can get something like this:

In the annotations panel, you see that area and length of annotation objects are calculated based on a dimensionality of the respective object. If you just draw a line, then the line by definition has no surface area. If you just put a landmark icon down, it has neither an area or a length.

You can add notes to individual annotations, and toggle the visualize by clicking on the “eye” icon on the right-hand side of an annotation

An annotation note has two properties: the note itself, and the annotation’s classification. By default, all annotations are placed in the “generic” category, but these can be extended just by entering names for them.

Pathology-specific annotation tools

Pathomation is a company created by pathologists… for pathologists (and by extension: everybody else who has any exposure to microscopic image material). We include the standard annotations tools because they’re… well… standard.

But quickly we concluded that things that make sense in, say, Adobe Photoshop or GNU Gimp, don’t necessarily make sense for our specific type of data. In other words: do let us know the last time that you were able to delineate the shape of a Drosophila embryo with a rectangle tool or could fit a tumor mass into a perfect circle.


First off: we provide two polygon-annotations.

With the default Polygon annotations, you can set points one by one until you’re satisfied that you indicated your region of interest.

The Closed Freehand is a variation on this theme. Only now you’re not indicating the boundaries by your polygon one by one, but you do it with one continuous motion. Keep pressing down the mouse button while you’re drawing, and when you lift your finger, you’re done.

Indicating a tumor region needs to be precise. A person’s diagnosis, subsequent treatment, and ultimately survival chance can depend on it. The problem then becomes: how to combine drawing a large area at a high-enough resolution?

That’s why we have the compound freehand. With that, you can draw the edges of your region of interest in segments. You delineate one border, pan / zoom a bit further into the slide, annotate more, pan / zoom… etcetera until all your segments reasonably mark your target area. Then you click on the finish button, and the individual segments are automatically glued together into a single annotation.

Cell counting

If you’re into the business of counting cell, then Multipoint is the annotation that you want:

Once the tool is enabled, you can keep clicking on features of interest, and rather than converting all of these in individual point-annotations, you end up with a single annotation with n points. Combine this with the possibility to assign a classification to your annotations, and you end up with a very powerful tool to e.g. count mitotic- versus non-mitotic spindle figures.

How it works

Annotations created in are stored in PMA.core. PMA.core stores all annotations in its back-end database, along with audit-trailing information that includes who made the annotation and when.

The annotations can at any time be exported in a variety of formats, including Well-known text (the format used by PMA.core internally), Visiopharm mld files, Indica Labs HALO annotations files, Definiens/Aperio xml files, and ‘plain’ csv files.


Where to from here?

Today we continued our exploration of and looked at annotation.

In our next episode , we’ll go deeper into, and talk about capturing metadata and forms. We’ll also explore our virtual tray more.