View Navigator

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FAQ

View Navigator

QiTissue has the ability to load in and display very large images. The View Navigator provides a small overview of the entire image with a rectangle indicating the current Field of View (FOV). Click Reset View to restore full view of the image.

In the view navigator window, you can always see a reference to what is happening compared to the full image. The white rectangle in the View Navigator display itself is also draggable, so you can directly drag it to a region of interest.

Clicking Fit Selected will zoom into any selected cell outline. This is useful to quickly hone into a selected cell and to precisely see the boundaries applied by the segmentation.

You can dynamically interact with other widgets while taking advantage of this feature, such as the Feature Table and Feature Plot. Just click on a row in the table, or a data point in the plot and click on Fit to Cell. Selecting the cell outline on the Image Viewer will jump to the table row or scatter plot point directly.


Adjusting Field of View

You can adjust the FOV in several ways:

The zoom scale slider (located at the top). Use by clicking and dragging left or right, or simply use the mouse wheel to zoom in and out.

Keyboard shortcuts, which can be found in the File menu under View → Zoom.

Navigation icons located on the top right of the Image View. Click and drag the magnifying glass up and down to zoom in and out (or click and hold control + command). Click and drag the second icon to move along the x and y axis (or click and hold command).

The effect of dragging both icons in 2D is shown here:

Trackpad gestures (Note that these must be unlocked in QiTissue → Preferences → Touch Interface and only function on a machine with a multi-touch trackpad)

To zoom along the z plane, pinch the trackpad. To pan along the x and y axes, hold two fingers on the trackpad and drag to move your FOV.


3D Mode and Height-Maps

3D exploration of an image is a semi-novel method for identifying heterogeneous specs. The feature which stands out in this view mode is the height-map. The height-map translates biomarker intensity into a scalable height. Spending time exploring the landscape of an image can provide a spatial context for the biological sample and help derive new, meaningful insights. Combine color channel blinking, image filtering, and other processing functions to create truly stunning perspectives.

You can use any images you generate to modulate the landscape. For example, augment a computed channel, such as cell density or distance maps, on top of the existing biomarker stains. Using a Logical scale is ideal when viewing these computed channels. This sequence can show mountains indicating T cells infiltrating a tumor, or point out where B cells and T cells are in close proximity to each other. This is a novel way to visualize high dimensionality data.  

While in 3D mode, you can also rotate your camera viewpoint by clicking and dragging the rotating arrow icon on the top right of an image.

Each effect is shown here in 3D mode:

As you become more advanced with navigation, you can utilize additional keyboard shortcuts. Hold down Alt+Drag to move along the image. You can also hold Ctrl+Alt+Drag to zoom in and out, and hold Alt+Shift+Drag to tumble when in 3D mode.

Some text showing these shortcuts appears at the bottom left of the screen whenever your cursor is hovering along the View image.


Image View

The Image View can be split up into multiple views for convenience. This way you can see different perspectives simultaneously, and add scenes to the sequencer from each one into one timeline.

Split Horizontal Image View

You can split the currently selected Image View either horizontally or vertically by going to the gearwheel on the top right corner of the Image View window. You can do this as many times as you like, and the new Image View will spawn with relation to the one that is currently highlighted. To remove a view, just click the X on the top left of the window.

Additional Split Vertical Image View