Day 2 – Looking at slides with PMA.view
Pathomation’s software platform for digital pathology consists of different components. Whatever your scenario is for digital pathology entails, chances are that you’re going to interact with virtual slides at some point. PMA.view is an excellent tool for end-users to explore slide collections. PMA.view runs on top of PMA.core, which was the focus of yesterday’s tutorial.
PMA.view is a web-based slide viewer. You launch it from your sandbox environment by clicking on the button.
Depending on your specific configuration, you should see something like this:
PMA.view uses a ribbon-interface, that is completely configurable with buttons and functionality if your choice, if so desired. Below the ribbon, a number of panels show, which are also flexible and configurable.
That “Default server” in the left “Side browser” panel is a reference to the PMA.core instance that you logged into yesterday. When you try to expand the triangle icon in front of it, you’re asked to log in. You can go ahead and do so with the account credentials that you used yesterday to log into PMA.core directly.
After logging in successfully (can use the password reminder function as discussed yesterday if you’re unsuccessful), you’re presented with a navigation tree that reflects the slides hosted in PMA.core.
The tree integrates your folder structure and your slides into a single list, which is different from PMA.core.
The slide browser panel has a number of buttons itself, which can be used to customized your viewing experience. Pick a folder from your tree with some slides in it, then hover over the various buttons to see their respective tooltip and try out their effect.
You can toggle automatic thumbnail previews, or opt to see the slides in a folder as a gallery rather than a list. You can also choose to use the slide barcode for previews, compared to the slide’s overview picture.
Clicking on a slide’s filename (or on a thumbnail when in gallery view) opens the slide in a viewing panel:
You can have multiple slides open next to each other in different tabs:
You can also have them spread out and organize them over different panels:
Time to turn out attention to the ribbon now. The “PMA.view” indication is a general menu that gives you access to commonly used high-level functions like changing your PMA.core password, consulting our manual, or accessing our helpdesk for bug reporting and customer support.
The first “real” group in the ribbon then allows you to quickly change the layout of your various panels.
“Simple layout” restores your panel configuration to just the Slide browser and slide viewer panels, whereas the second “Detailed layout” button allows you look at slide information and to adjust color representation (brightness / contrast / gamma) values as well.
The first button in the viewport group on the ribbon allows you to create extra (empty) tabs. You can then activate those tabs and populate them by selecting slides, or via drag and drop.
The viewport group on the ribbon allows you to control which information elements about a slide are available in the viewport.
The navigate group lets you quickly navigate to the next and previous slide within a folder, or jump folders altogether. This is useful when going through series of slides, where you want to have as much space as possible dedicated to your slide viewport, and even the slide browser panel can take up too much space.
Jumping folders is equally convenient. You may have your folders represent “cases”, and you don’t always need to look at all the slides within a case to reach an appropriate conclusion.
Buttons in the Navigate section have keyboard-shortcuts as well. You can see which ones these are by hovering over them (they’re included in the tooltip).
The “slide” group is self-explanatory and lets you cycle through various standard magnifications.
Working with grids
Working with different slides in different viewport panels isn’t always what you want. It’s very convenient for keeping reference slides close by, but sometimes you want to look at a group of serial sections together. For those and other instances where navigating multiple slides simultaneously, PMA.view supports grids.
Note that when you created a new viewport tab, the title in the tab already hinted about them: it would show that you created a 1×1 grid.
The easiest way to start working with grids is by opening an entire folder as a grid. The folder may represent a case, and PMA.view will automatically detect a grid configuration that’s appropriate, based on the number of slides in the folder.
You can choose where you want to grid, if you want to keep the current slide(s) you’re looking at already, as well as make a subselection of the slides in the folder (some of them may be rescans, in which you case you wouldn’t want to include the original ones probably).
In our example, a 2 x 2 grid springs up and lets you navigate the slides individually, or simultaneously:
In order to enable synchronous navigation, you toggle the setting in the ribbon
The other buttons in the Grid group on the ribbon mostly have to do with the grid layout. You can choose standard grid configurations of 2 x 2, 3 x 3, or you can revert to a single grid. Also useful is the function to pop-out one of the cells of the grid to a new tab (viewport panel) for more detailed inspection.
You can clear all cells in the grid with the click of a single button, and you can repopulate each cell in your grid using drag and drop from the slide browser.
In today’s episode we took you on a tour through PMA.view. There’s more to learn, and we’ll come back to it in a couple of days.
Tomorrow we’re going to spend some time first answering a question some of you may already have been asking: “This is all good and well, but how does Pathomation’s platform work with MY slides?”.