Pathomation tutorial series – 10 days of slides – day 10

Day 10 – Miscellaneous tips and tricks

On the final day of our tutorial series, we want to take the opportunity to present you with various small tips and tricks and that can help you get the most out of our software. There are many features in our different components that we haven’t told you about yet. In fact, during the writing of this tutorial series, more options became available as part of our regular development cycle.

PMA.transfer – new stand-alone version available

PMA.transfer is a great program to transfer slides between your local environment and PMA.core (both download and upload). But we received several reports from people saying that the greatest struggle was to get the required Java Runtime Environment (JRE) up and running.

We address this problem by now offering a downloadable version of PMA.transfer that already has everything you want in it, including the JRE. Download the zip-file, extract to a directory from your choice, point and click to the PMA.transfer.exe file, and you’re in business.

New in PMA.transfer is also that we’ve abandoned our PDF manual and replaced them by a wiki. You can get access to it through the Help menu, after which your favorite webbrowser takes you there.

We find the wiki format more enjoyable and user-friendly than the rigid PDF documents. Our QA department has given this new format a thumbs up as well, and we’re now in the process of converting all of our manuals into wikis.

The latest version of PMA.transfer as of writing is version 2.1.1 and can be downloaded from http://host.pathomation.com/pma.transfer

PMA.studio tips and tricks

If PMA.studio was not part of your sandbox installation, contact us so we can add it.

Search

As you get build your slide collections and your directory folders becomes more complex, you find yourself in a search function. PMA.studio has you covered!

The search panel let’s you select which PMA.core server(s) to search, as well as specify an initial subfolder. The latter is particularly handy if you have millions of slides spread over hundreds of projects, each represented by their own directory (and subdirectory structure).

You can have multiple queries run at once. Queries can finish one before the other, and you can even retrieve previously run queries.

Results can be exported to CSV, or be sent to the tray: a particularly useful concept in PMA.studio that let’s you manipulate arbitrary groups of slides.

Using the virtual tray to manage arbitrary slide collections

We introduced you to grids in our earlier tutorial on PMA.view (all features from PMA.view are also available in PMA.studio). Grids have limitations though. When you run a search that returns fifty of so results, it’s impractical to display all of those as a single grid.

What happens when you send a person down to the slide archive to retrieve some slides for you? The person probably comes back with a tray of slides for you to further select from and examine.

To faithfully replicate this process, we implemented a virtual tray functionality in PMA.studio. You can toggle the tray’s visibility via the configure tab on the ribbon.

The screen below shows several concepts at the same time: we run two searches, our tray contains a couple of slides already, and we’re adding a select number of slides to the tray from the most search query.

Once you have your slides in the tray, you can choose to either show them visually (thumbnails), or as a list. The list can in turn be exported to a CSV file for future reference (you can re-load your tray via this mechanism, too).

One more screenshot: this time you see the tray as a list.

We selected a subset of slides from our grid and converted them into a grid in the right-hand panel. You also see the exported results in Excel.

Integrate with PMA.start

PMA.start is our free software for local slide viewing. It supports all file formats that PMA.view and PMA.studio support, but is limited to the slides on your hard disk (as well as externally connected hard disks). It comes in Windows, Mac, and Linux flavors.

PMA.start is a free product, which means it doesn’t have the same features PMA.studio has. So what do you do when you want to use PMA.studio to look at your local slides? There’s a button for that!

When PMA.start is found running on your local computer, it will show up as a new PMA.core tile server in the slide navigator panel. You can use this e.g. to create grids that compare slides from your local system with reference slides on the server.

The screenshot below shows both interfaces side by side:

Pathomation programmability

As we tried to show you in this tutorial series: there is a LOT you can do with the Pathomation software platform. But there’s even more: Our software looks a specific way, and certain actions can certainly be organized different. For the ultimate power-user then, we provide several Application Programming Interfaces (APIs) and Software Development Kits (SDKs).

We currently offer four:

  • Our front-end workhorse is UI, a JavaScript set of components for anything to do with slide visualization. Most recognizable are the viewport and slide gallery controls, but there is a lot more you can do, from hierarchical browser to building custom annotation interfaces for specific workflows.
  • python is a Python SDK. We use this ourselves a lot to do custom scripting, but our customers also get to work with it themselves.
  • java is a Java SDK. It’s used for back-end integration tasks in J2EE environments.
  • php is for PHP developers. Bad rep or not, the language is still one of the most convenient and easiest to learn, and you can get thing like proof of concepts (POCs) done fast in it!

We take our own medicine, too: everything we’ve shown you in this tutorial series, was built with our own tools. When you see thumbnails, they’re usually show through PMA.UI’s gallery control. PMA.transfer makes heavy use of the PMA.java SDK. PMA.slidebox is a combination of PMA.UI and PMA.php.

What if e.g. you want an interface with two slide galleries to pick from? This is exactly what we did when the Liver Metastasis Research Network approached us. The website is no longer available, but the paper is available through PubMed.

In closing

After looking at several individual Pathomation platform components in this tutorial series, today we took a more holistic approach and presented you with quick tips and tricks. We also showed you showed you how the different components can work together.

If at any moment you feel you want a more hands-on introduction to Pathomation products, you can make an appointment with us via the contact us form to get a walkthrough through the website we set up for you. We’d be happy to share strategies customized to your digital pathology goals.