The story of the three Qs

In this article, we explain how Pathomation was recently able to assist its one of its customers with Performance Qualification tests for a new slide scanner.

At our customer’s lab, each piece of equipment that they take into operation, goes through a rigorous qualification pipeline before putting it to work for day-to-day lab activities.

This goes for slide scanners as well.

The qualification pipeline (the “validation procedure”) consists of three steps:

Installation Qualification (IQ)
Operational Qualification (OQ)
Performance Qualification (PQ)

The first step is straightforward: you’re asking yourself if the scanner can scan your slides or not. Is the type of glass slide that your lab use, in combination with the coverslip, compatible with the new scanner? Is the barcode on the slide label scanned properly, too? What about (automated) tissue detection?…

The second step is operational qualification: can the new equipment handle the edge parameters of your day-to-day operations? If you plan to feed the scanner up to 400 slides per day; will that work?

The third step in the validation can be somewhat subjective, and it’s here that Pathomation’s software platform came in particularly handy.

Performance Qualification

Performance Qualification (PQ) is a test procedure that takes place in order to verify if a new piece of equipment is good enough to be put to work in the daily workflow of a company. It happens after the hardware has already gone through IQ and OQ.

Our customer recently wanted to know how their various scanners compare to a new one in terms of speed. They took a representative set of slides, divided it in three groups (“requests”), and then put each scanner to work.

their various scanners compare to a new one in terms of speed. They took a representative set of slides, divided it in three groups (“requests”), and then put each scanner to work.

In the vendor’s viewer software, one of the parameters that could be seen was “scanning duration”. Considering the side of the dataset however, opening each slide individually in the viewer software, noting down the scanning time, recording it into an Excel sheet etc., would have been a very tedious task.

So they turned to Pathomation for help: Can Pathomation’s software be used to create a table with all scan duration values for all scanned slides?

Our API

Pathomation’s API offers a get_slide_info() call. We used it in our first article on business intelligence to extract specific bits of information with it. The method be default returns a nested hierarchy of information.

But not every scanner exports the same information. Some of the slide information we expose ourselves through ImageInfo, some not. This is because vendor 1 exposes (A, B, C, D, E), vendor 2 exposes (A, B, F, G, H), vendor 3 exposes (A, B, C, I, J, K, L) etc. Therefore, Pathomation offers the common denominator information only, something like (A, B, C).

In order to maintain some standardization across the different vendors, part of the returned information by get_slide_info is a MetaData array that contains key-value pairs that may or may not be provided by your scanner vendor.

As it turns out, we didn’t have the scanning time in there yet, but because of the already provided structure, it was straightforward to add it.

Like our first business intelligence exercise, we then write a wrapper method to extract the scanning duration as we need it:

def get_scanning_duration(slide_ref):
    info = core.get_slide_info(slide)
    meta = info["MetaData"]
    for meta_el in meta:
        if (meta_el["Name"] == "ScanningDuration"):
            return meta_el["Value"]
    return -1

The remainder of the script is straightforward:

Loop over the different scanner output
- Foreach scanner (“request”), get all the slides (recursively in our case)
  - Foreach slide, extract the scanning duration
Wrap all output into a Pandas dataframe structure
Export the Dataframe to a spreadsheet

A word about that last step. On occasion, people have called us old-fashioned for this one. Surely Excel is spread wide and far enough by now so that it can be considered a de facto “standard” file format, too, can’t it?

I disagree. I still prefer to use csv instead of Excel. Why? Because csv files are simple, and transportable to many other platforms and applications. Our data in this case consists of a single table with three columns. It’s simple. We don’t need a complex data format to store this kind of data.

Generating fancy file format output is not part of the assignment here. Keep It Simple.

Our final code looks like this and can be downloaded as a Jupyter notebook, so you can play around with it yourself.


server = "http://***/***"
user = "***"
pwd = "***"
print("Session initiated ", core.connect(server, user, pwd))
requests = ["RQ105", "RQ204", "RQ695"]
base_folder = " Images/pq"
print(len(core.get_directories(base_folder)), " subfolders detected in root base folder", base_folder)
s_times = []
for req in requests:
    print(base_folder + "/" + req)
    for slide in core.get_slides(base_folder + "/" + req, recursive=True):
        s_times.append({"slide": str(slide).replace(base_folder, ""), "scan_time": get_scanning_duration(slide), "request": str(req)})
scan_times = pd.DataFrame(s_times, columns=["request", "slide", "scan_time"])
scan_times.to_csv("scanning duration.csv")

What about the results?

We can import the resulting CSV file in Excel and see what it looks like:

As we’re interested in comparing the different scanners to one another, one direct way to do this is with a pivot-chart.

These are the results. What do you think? Do all three scanners perform equally? Does the new scanner pass performance qualification (PQ)?

Your challenge here

This is how Pathomation works with its customers.

Our philosophy has been and remains to develop local, and then scale as you handle more complex scenarios. You do not need the commercial version of PMA.core to get to work with the code in this post. The Jupyter notebook that comes with this blog post is suited for use for both PMA.start and PMA.core.

Do you use Pathomation software in your daily workflows already? Tell us your business intelligence challenge and perhaps we’ll address is in an upcoming post!

So what if you “just” want to show your slides?

Education is one of the main application domains of digital pathology. And there are many instances where you just have a couple of slides that you want people to look at. When Pathomation first became involved in deploying its software for facilitating seminars, we used PMA.view.

But while it’s possible to do this, PMA.view is not a good solution for this particular problem:

People still need to login in PMA.view
PMA.view requires telling people where to navigate to (which root-directories / paths); your root-directories on the PMA.core side of things may not exactly reflect the content that you want people to see.
PMA.core is folder-based navigation, and PMA.view is too. This means that the concept of a case (a group of slides belonging to a patient or experiment) is not intuitively represented
neither PMA.view nor PMA.core support any of the visual cue-elements that we’ve all gotten accustomed to in recent years such as avatars.
The learning curve of PMA.view is still too steep for people that just need to look at slides. PMA.view is overshooting for what you want people to actually experience

How did people used to do it? They traveled to conferences with a slidebox in their hand luggage. Within the slidebox; neatly organized slides, sorted by case. We don’t want to be sensational here and say that the slides got lost all the same, or that they broke all the time, or got confiscated by security in a post-9/11 world (glass slides + ninja pathologist = impromptu shiroken?).

But: things could happen when traveling with physical slides, and the most likely issue was probably still somebody forgetting to take their slides with them in the first place!

Also: when traveling with physical slides you depend heavily on the organization’s talent of providing and calibrating multi-headed microscope equipment. As more people attend, aligning all the optics of these becomes ever harder, and for large groups this is just impractical.

Cue PMA.slidebox

So we got thinking… If people are used to physical slideboxes, why not just make a virtual slidebox? This is exactly what PMA.slidebox is and does!

PMA.slidebox, like all our software, relies on PMA.core. It means that you can use all the great features of PMA.core (different root-directories, access control), without having to explain it to your audience.

All your audience sees, without to register or login or need to install or download anything (zero footprint) is this:

So how does it work? PMA.slidebox shows up to four collections in the top-left corner of the screen (screenshot only shows three). When you select a collection, you see the “cases” appear underneath it, along with the slides for each “case”.

We put the word “case” between quotes deliberately because you don’t have to set it up this way. You can have a simple list of slides without any hierarchy or structure to it, and PMA.slidebox will pick it up. Similarly, if you only have a couple of cases, you could turn those into individual collections, and present them as such.

What you want to show and how you want to show it is completely up to you. It’s just like a real slidebox: you put the slides in that you want, and you organize them the way you want them, too.

Want to give it a go yourself? Here’s an example how such a virtual slidebox works in practice: http://host.pathomation.com/p0022_slidebox/

Configuration

PMA.slidebox is flexible. It is hosted on a website, somewhere (can be on your infrastructure, or on ours). If you don’t have PHP, we can configure it for you; but if you do, you can configure everything by yourself via a configuration panel.

What you first need to do is decide how you want to have everything structured. You can build a hierarchy of up to three deep, with the following levels:

As you have only 4 cases in the above screenshot, you could simplify your hierarchy like this:

While PMA.slidebox is flexible, we should point out that it is necessary to have some kind of hierarchy at least. You cannot just dump all your slides into a single folder and expect the software to figure it out from there.

Note: if you do have large repositories of slides, and you want structured case creation and organization, you should have a look at PMA.control.

Here’s what the setup looks like when your spread your cases across only two collections:

And here’s what that same group of slides looks like, but this time with each case being defined as its own separate collection:

In closing

With our PMA.slidebox product, Pathomation solves the problem of mass-distribution of slide collections. When you just want to share your slides with people in a somewhat organized (collection and cases) fashion, PMA.slidebox is the perfect solution for you. The easy to use configuration panel behind the front-end makes it a breeze to point to the exact content that you want to display, and under no circumstances does the end-user have to do anything else except click on the URL that you provide them with.

Find out more about PMA.slidebox at our website at http://www.pathomation.com/pma-slidebox.

Month: March 2020

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