Pathomation tutorial series – 10 days of slides – day 1

A brave new world

Getting started on a new digital pathology platform can be hard, and it’s our job to work with you to make it as easy as possible to achieve success with Pathomation.

In an online series of 10 articles, we’ll present you with simple tutorials, tips and tricks to help you get the most of your trial-period (be it a sandbox, beta-test, or production environment), as well as offer you a chance to submit your own feedback to us.

User registration and PMA.core

Pathomation’s software platform for digital pathology consists of different components. Whatever your scenario for digital pathology entails, chances are that you’re going to interact with virtual slides at some point. Because the concept is so central, interaction with digitized slide material became the core component of our platform and therefore we call it PMA.core.

PMA.core in essence does 4 things:

  • Allow you to look at slides, regardless of how they were acquired
  • Manage and register (new) meta-data for slides, including 3rd party annotationsµ
  • Organize a user database (integration with LDAP is possible, too)
  • Keep track of user permissions and who does what at any given time

Because PMA.core is user-centric, the first thing you need to do in your sandbox if create a user account for yourself. In fact, if you haven’t done this yet, the landing page will tell you this is first thing for you to do (and now you also know why).

In case you went through Pathomation to request a product trial or participate in our beta-program, you were given your personal landing page, which contains a self-registration feature under the heading “Make a new user account”:

After you enter your username and email address, your sandbox environment will automatically generate a randomized password for you.

The password is shown on screen, and is also sent to your email.

If you didn’t get the email, check your spam folder, and make sure you typed the email address correctly.

Note that the email does NOT remind you of your username. If you’ve forgotten that one for some reason, you can click on the “List what users already exist in your sandbox” link, in the same section:

Using PMA.core for the first time

Now that the account formalities are out of the way, you can go ahead and log on. Click on the “PMA.core” button under the top “Sandboxed products” section of your landing page, and a login dialog will appear:

Enter the credentials created earlier, and you’re presented with a start-screen that looks like this:

There’s not much to be seen here yet. In days to come, we’ll familiarize you with various aspects of PMA.core.

For now, let’s just look at some virtual slides. Click on the first “Images” button (almost right underneath the “Home” indication).

You now find yourself in the “Image management” section of PMA.core. You should see a tree structure with three root-directories (more on what these are specifically in a later post). Expand the top “Cases” leaf in the tree and keep drilling down until slide references appear in the listbox next to it.

Upon clicking on any of the slides, you’re presented with different kinds of information about the slide: its size, what type it is, and whether it has associated meta-data.

Looking at slides

Clicking on the thumbnail of the slide, brings up a slide viewer window.

Here are some basic properties of our viewer:

  • Clicking down on the left mouse button and dragging the mouse around, lets you pan around the slide
  • Double clicking on any point, zooms in on the area surrounding the point where you clicked
  • Your mouse scrollwheel works equally well for both zooming in and zooming out of an area of interest
  • Dragging the mouse while holding the shift-key on your keyboard is called shift-drag. It allows you to draw a specific rectangle that you like to zoom in on. Releasing the mouse key fits your selected region within the browser window as well as possible.
  • Rotating a slide is possible, too. Hold the Alt-key on your keyboard while dragging the mouse around.

Some other notable buttons on the screen:

And there you have it.

Yay, you did it!

In today’s first episode we showed you that Pathomation’s software platform offers a secure environment for digital slide interactions:

  • You learned about PMA.core, or central component for slide management and visualization
  • You created your own user account into PMA.core and used it to authenticate yourelf
  • You learned about the Image manager and how to browse and inspect slides
  • You looked at a slide and became acquainted with the various aspects of our slide viewer

The viewer interface offered through PMA.core is pretty basic. In our next post, we’ll explore PMA.vue, a powerful viewing environment that lets you explore slides in more powerful ways than what we’re able to demonstrate here.

You can read about PMA.core at http://realdata.pathomation.com/a-look-at-pma-core