It’s coming, it’s coming, it’s coming, it’s coming…

And we’re really excited about it!

We’re in the process of wrapping up PMA.studio. This is going to be our flagship product for the next three years. It’s got everything a microscopy enthusiast needs, ranging from powerful viewport manipulation options, over annotations, to live conferencing. Remember our earlier article about how PMA.core handles (external) slide meta-data? All of that and more is in there, too.

In this blog post, we want to give developers as well as customers in our OEM and reseller program a sneak peek at PMA.studio and specifically focus on the opportunity for custom add-on development and white labeling.

PMA.studio is currently in testing phase for various use cases already, ranging from comparative validation studies to enterprise-wide deployment as a central histological information cockpit. If you are interested in joining the effort and helping us track down last minute bugs, do shoot us an email and we can see if you’re a good fit for our beta-program.

You can find more information about PMA.studio itself in the landing page that we’re building for the software at https://www.pathomation.com/pma.studio.

Administrative console

PMA.studio has a separate interface apart for administrative tasks.

In the administrative console, you can register any number of PMA.core instances to be used by PMA.studio to retrieve slides from. Once in use, for each registered PMA.core instance, you can see what users have sought access to it.

There’s a general dialog where you can set system-wide settings, like the address to contact in case of trouble, or the company / institute logo to use. This is where white labeling starts.

Like for PMA.view 1.x, the administrative console in PMA.studio can be used to customize the ribbon interface at top of the interface. The syntax is XML. We don’t have any formal definition of the format, and typically work with customers to get the result they want.

You can play around with the XML code yourself if you want. The default toolbar provides enough example code to allow simple re-arrangements of buttons and move features between different tabs.

If you run into trouble, there’s always the option to restore the code back to a default toolbar.

Custom annotations

PMA.studio supports annotations. We have a separate tutorial on the subject as part of our beta-program.

There are situations where you don’t want users to go off and make their own annotations at will.

You may want your pathologists to annotate invasive tumor margins or necrotic areas for a study protocol. It’s useful then that people align, and everybody uses the same color scheme. So in addition to providing standard annotation tools, it’s possible to define buttons on your toolbars w/ pre-set attributes and parameters.

Here’s a great example of a project we participated in recently, for which participants had to indicate six different types of tissues / cells:

The underlaying XML for this extra ribbon tab is as follows:


<Tab label="NKI" hint="custom ribbon tab" name="nki_annotations" enabled="true" visible="true">
    <Ribbon label="Total TLS" width="30%">
        <Tool type="buttons" size="large">
            <Command name="preset-peri_mat" icon="an_m_peri_tls.png" hint="Total # mature TLS (peritumoral)" label="Peritumoral, mature"
                pma-classification="peri mature"
                pma-shape="ClosedFreehand"
                pma-color="#ffff33"
           />
            <Command name="preset-intra_mat" icon="an_m_intra_tls.png" hint="Total # mature TLS (intratumoral)" label="Intratumoral, mature"
                pma-classification="Intra mature"
                pma-shape="ClosedFreehand"
                pma-color="#cccc00"
           />
           <Command name="preset-peri_immat" icon="an_im_peri_tls.png" hint="Total # immature TLS (peritumoral)" label="Peritumoral, immature"
                pma-classification="Peri immature"
                pma-shape="ClosedFreehand"
                pma-color="#999900"
            />
            <Command name="preset-intra_immat" icon="an_im_intra_tls.png" hint="Total # immature TLS (intratumoral)" label="Intratumoral, immature"
                pma-classification="Intra immature"
                pma-shape="ClosedFreehand"
                pma-color="#ffff66"
            />
            </Tool>
        </Ribbon>
        <Ribbon label="Pre-sets" width="30%">
            <Tool type="buttons" size="large">
                <Command name="preset-necrosis" icon="an_necrosis.png" hint="Tumor" label="% necrosis"
                    pma-classification="Necrosis"
                    pma-shape="ClosedFreehand"
                    pma-color="#aa0000"/>
                <Command name="preset-fibrosis" icon="an_macro.png" hint="Tissue" label="% fibrosis"
                    pma-classification="Fibrosis"
                    pma-shape="ClosedFreehand"
                    pma-color="#00aa00"/>
            <Command name="preset-via_tumor" icon="an_tumorcells.png" hint="Tissue" label="% viable tumor cells"
                pma-classification="Viable tumor cells"
                pma-shape="ClosedFreehand"
                pma-color="#000000"/>
        </Tool>
    </Ribbon>
</Tab>

The pay-off of this kind of configuration is two-fold: the protocols are consistently executed as intended. In addition, the training needed for novel users to interact with the software is reduced because they only have a few options to choose from. Less can definitely be more in these scenarios.

Configuring the panel layout

PMA.studio organizes its content across different panels. The layout of PMA.studio is a lot more powerful and flexible than in PMA.view 1.x.

All panels can be turned on or off via the Configuration tab on the ribbon. In addition, the admin console can be used to pre-determine the layout and panel organization when people first log in.

In its simplest configuration, you’re navigating slides and looking at them one by one:

You can add various information panels as you see fit to get to something that looks more like this:

Like with the ribbon customization and pre-defined annotation controls, you can pre-set PMA.studio’s panel layout. Again, you’re looking at XML snippets.

The layout from the latter screenshot is then defined as follows:

Iframe panels

A special type of panel is the iframe-panel. With these panels, you can virtually load any website or page that you want within a pre-defined PMA.studio panel. You can define your own panel through the Layout configuration button on the ribbon:

A pop-up dialog appears and let’s you specify the title of the panel, and the URL you want it to load.

In our example we took a promotional video for our own PMA.slidebox product (more on that later), but you can put just about anything in there.

The result looks like this:

You can pre-define these custom iframe-panels any way you want through the admin console.

<Component name="IFrame" label="Pathomation video" url="https://www.youtube.com/embed/VsiGz8ykuEo"/>

Respective parameters that indicate the current state of the active viewport in PMA.studio are passed along automatically, like this:

http://www.server.com/app/page.php ?server=%PATH%TO%PMA%CORE% &path=%FULL%PATH%OF%SLIDE% &sessionId=%SESSION%ID%

Last but not least: a product pitch

We wrote earlier about PMA.slidebox.

This week, we’ve officially started promoting this product. We updated the landing page for PMA.slidebox, and the first demonstration videos are available through our YouTube channel.

Like with everything we do, we’re very excited about being able to package a ton of useful functionality in nevertheless compact product offering. Do have a look at our demo portal for PMA.slidebox and let us know if this something you, too, are interested in, too!

What is slide meta-data?

In order to know to interact with something, we first need to know what it is. Or, at least, we need you to know what it means for us. Just so we’re clear what we’re talking about.

For the sake of this article, we distinguish three different kinds:

Intrinsic meta-data: information stored within a slide’s file format. A trivial example is the slide’s pixel size, and a more advanced feature is the time it took the scanner to produce the slide.
User-captured meta-data (forms): Pathomation’s central tile server component, PMA.core, allows for the definition of table structures. Forms are a basic data structure in PMA.core that’s picked up again and used to capture and present user-attributed data in other several Pathomation platform components, including PMA.studio, PMA.slidebox, and PMA.control.
External data: if you have tons of external data in a separate repository and want access to it through the Pathomation software platform for digital pathology and virtual microscopy, you can link to it in real-time.

Below you can find an overview of what kind of meta-data is supported by what component and in what capacity

	Slide info	Forms	External data
PMA.start	Read	Not supported	Not supported
PMA.core	Read	Define / read	Read
PMA.view	Read	Not supported	Not supported
PMA.studio	Read	Read / write	Read
PMA.slidebox	Read	Read / write	Read
PMA.control	Read	Read / write	Read

Slide info

Intrinsic slide meta-data can be shown in PMA.start by clicking on the filename in the viewport.

In the upcoming versions of both PMA.view and PMA.studio, we provide a separate info-panel for this.

There can be more slide info available than is actually shown in our various front-end interfaces. Some information is really specific, too specialized, or irrelevant even to show to most users. Other fields are scanner-specific and don’t make sense to include on a systematic basis.

At the API and SDK level, we provide dedicated SlideInfo calls that return full hierarchical dictionary structures that do give exhaustive slide information and can be consumed as you see fit for your specific application or workflow.

Data with a twist

Forms are defined in PMA.core through the form editor.

PMA.core’s forms support trivial datatypes like text or numbers (of course). We also offer scientifically relevant twists on traditional data capture. An example is that numerical data fields allow the option to be recorded as “below detectable limit”, since it’s very hard to prove that something is not present in a sample. Oftentimes, a numerical zero just means that our detection apparatus just lacks the sensitivity the unmask the presence of a specific phenomenon.

What can you do in forms? Pretty advanced things. We can model the CAP-recommended cancer protocols as PMA.core forms.

PMA.core offers different ways to interact with forms, but it doesn’t provide a data entry module. That’s because it doesn’t really make sense to enter data at this level. Data entry is done in the context of an application or workflow. Our upcoming PMA.studio will support data entry, and PMA.control offers several interaction modes. Underneath, PMA.control interaction modes rely on data stored as PMA.core forms.

You can ask PMA.core to generate a spreadsheet template based on a select folder of slides and a particular already defined form.

At Pathomation, we pride ourselves to be a truly open platform, so PMA.core offers several data formats to export captured form data to, including CSV, XML, and ARFF.

Use cases for external data

Imagine that you organize a toxicology experiment with a rodent population. In a separate database, you’ve been keeping data about each specimen’s vital statistics, dietary and behavior observations, as well as their phenotypic expression and genotypic make-up. Observations happen daily, so that’s 1750 new records per week.

You take weekly biopsies of the animals to monitor their response to a new drug you’re testing. The biopsies are prepared and stained in triplicate (good for a total of 750 new slides per week), and each slide has a barcode that can be used to trace back to the original individual animal. Your slide scanner takes care that the barcode is encoded in the slide’s filename.

Both the slide population and the separate database keep evolving. Replication between your database and a PMA.core form is considered at some point, but deemed inefficient and error-prone, because we are talking about experimental and evolving data structures here.

The solution is to define an external data source in PMA.core. This goes in two steps: first a connection string is defined to connect to the database server.

Next, the external connection is used to formulate any number of queries against.

Data can be previewed within PMA.core, and subsequently is automatically propagated to other environments like PMA.studio.

External data are everywhere. They can be in proprietary databases as in our example above, but they can also be in a (AP)LI(M)S, VNA, PACS, or EHR system. In all those cases, replication is hard and impractical at best, and can even lead to data inconsistencies and errors at worst.

The Pathomation platform for digital pathology and virtual microscopy allows for a more elegant solution.

Month: October 2020

Customizing the next generation of slide viewer software