Ribbon
The Visiopharm Ribbon includes a set of tabs, one for each installed Visiopharm module. These tabs we will refer to as Module tabs. Each module tab contains some general buttons, and some module specific controls. Within each module tab, the graphical buttons and controls are grouped by functionality.
From the Visiopharm Ribbon, you are able to select a module by clicking the module tab or access general settings from File.
The Visiopharm Ribbon also includes a Quick Access Toolbar, which includes shortcuts buttons for undo/redo, saving your data and Full Screen-mode:
| Icon | Description |
|---|---|
 | Saves all data to the current place in the database. |
 | Undo the last action. (Ctrl + Z) |
 | Redo the last action. (Ctrl + Y) |
 | Toggles Full Screen-mode. (F11) |
 | Open image |
 | Reload/update the results |
 | Dropdown menu allowing you to customize which buttons to show in the Quick Access Toolbar. If opened, it expands as seen below. |
The general groups in all module tabs are:
- Overlays
- View
- Data Tools
Overlays group
The Ribbon includes the Overlays group. From the list, you can show, hide and control the transparency of individual overlay types (ROIs, Labels, Annotations, Measures, Heatmap outputs and Atlas) in the working area.
The Overlays group also includes the master transparency control which is the large slider next to the list. The master transparency control overrules the individual transparency controls of the overlay types.
- Control the transparency of each overlay type by clicking and dragging the opacity slider left or right
- Clicking once on the slider will hide/show the overlay type.
- Click the trashcan next to and overlay type will delete all overlays of that type.
Press Ctrl + L to turn the overlay on/off.
The Heatmap overlay is only visible if a heatmap output is saved with the image.
View group
The View group includes some of the useful tools and buttons regarding the current displayed image. The View group contains the three items shown below.
| Item | Description |
|---|---|
| Results | Show/hide the results window |
| Slide ID | Show/hide the slide ID |
| Navigator | Show/hide the Navigator |
| Histogram | Show image Histogram |
| Image Properties | Show image information dialog |
| Rotation Options | Opens the Flip and Rotate menu |
Synchronize Views group
You can open multiple images simultaneously by selecting two or more images and pressing Alt+Enter.
| Item | Description |
|---|---|
| Lock | Move and zoom is syncronized between the images |
| Auto | Automatic allignment |
| Reset | Reset to default zoom and allignment |
Color Adjustment
The Color Adjustment menu is opened by selecting Color Adjustment in the View group in the Ribbon.
The Color Adjustment menu lists all available color bands from the image and allows for a quick selection and visualization of all or just specific bands/channels of interest.
-
You can save the changes made to the image you're working on. It is also possible to save the color adjustment as a configuration. These configurations can be loaded to other images by clicking load, and selecting the desired configuration in the menu by either double-clicking it or by clicking load again. If you want to reset the image, you can click on reset image.
-
You have the option to either work in the channels from the image, or create groups.
-
You can enable or disable viewing of specific colors by clicking on the eye. The number next to the eye tells you the intensity of the color on a specific pixel. Clicking the topmost eye hides or shows all channels.
-
Adjustments made here will change every color band, unless a specific color has been selected. Your changes will show in real time on the image.
The Color Adjustment dialog controls the way images are displayed. By using the Color Adjustment dialog, the user can change brightness, contrast etc. For color images, the properties can be adjusted individually for each color band and the bands can be hidden or shown individually. Furthermore when displaying only one band the image can be shown in several pseudo colors.
Global / Band adjustments controls the adjustments made to the image, including Gamma, Contrast, Brightness, and Min/Max levels in %.
- Gamma is shorthand for gamma correction and can be adjusted to encode or decode the luminance values of the selected channel(s).
- Contrast and Brightness can be adjusted to change the contrast or brightness respectively of the selected channel(s).
- Min/Max % adjusts the distribution of light in the selected channel(s) based on the range between the min and max values.
Groups allow you to create groups for specific color channels, which can be useful if you're working with an image with many channels, and you're only interested in certain channels. If you click on group under channels it will look like this:
From here you're able to create groups with the channels you wish. A channel can be incorperated into any number of groups.
When a group is selected, only the channels you have selected for that group will be shown in the image.
Renaming of channels
Start by opening the Color Adjustment Tool.
Then click on the channel name that you wish to rename. Update the name to your preferred name and hit enter. The new name is now shown; however, the original channel name is still visible in grey.
Update all the channel names as needed and finally save the channel renaming to a color profile through: Save to Image, Save as New Configuration or Update Configuration.
When the configuration has been saved it can be be loaded to other images of the same assay.
It is generally advised that all name changes are performed before the cell segmentation and output generation steps for subsequent analysis. This assures that all name changes are subsequently passed through to all workflows and readouts. Any name chanes performed after the output generation are not passed through to the database results and require a re-analysis.
Data Tools group
The Data Tools can be found in any of the module tabs.
| icon | Description |
|---|---|
 | Open the Phenoplex Guided Workflow Tool |
 | Open the Explore/QC results Tool |
Show/Hide the Ribbon
You can show/hide the ribbon by double-clicking on the active tab e.g Home. This is useful when you want to maximize the working area, or for taking screenshots.