Navigation between multiple images

In ilastik 0.5, multiple independent images can belong to the same single project. When using the classification module it is useful to train on several images, representing the variety of the whole dataset (training set), and then to view the results of the prediction on other images kept as test set.

Navigating between images

Using the select image pulldown menu in the upper right corner of the window, we can jump to different images. Using the scroll wheel over the pulldown menu allows cycling through all images.

All of these images can be labeled simultaneously in the classification module, and the prediction is calculated for every image belonging to the project.

Navigating a volume image (3D, 4D or 5D)

  • Jumping to (x,y,z) directly.
    To jump to a specific (x,y,z) position, use the navigation control spinboxes on the lower right of the window.

  • Jumping to a specific time and channel.
    For a dataset that contains multiple time slices and/or multiple channels, the navigation control spinboxes look like this:

    The "Edit channels" button brings up a dialog relevant for the classification module:

    Here, the channels used for feature computation can be selected. If a channel does not contain information that is relevant for the classification problem it is better to not include it since it will only introduce noise and increase the memory demand; however, in settings with many multiple channels, the random forest classifier might be able to exploit information which is invisible to the human eye, in this case performance improves by including channels.
  • Slice intersection indicators.
    The slice intersection check box toggles the red, blue and green lines which indicate the slicing position (x: red, y: green, z: blue) in the three slicing views.
  • 3D view.
    The 3D view shows the coordinate system (again, the red, green and blue arrows indicate the direction perpendicular to the x, y and z slicing directions) and the current position by the intersection of the three slicing planes.

    Each plane is outlined in red, and the intersecting lines are shown in black. When hovering over one of the planes, it is shaded in red, green or blue.

    Dragging the plane changes the slicing position.
    With the X, Y and Z buttons just below the 3D view the visiblity of each slicing plane can be toggled to allow easier grabbing of those planes which remain visible.

Navigation-related keyboard shortcuts

  • Zooming/panning.
    To zoom, hold Ctrl pressed while using the mouse wheel; to pan, move the mouse with the middle mouse button pressed.
  • Going forward/back in a particular slicing direction.
    With the mouse over one of the three slice views, use the mouse wheel to move forward/backwards through the stack. To use the keyboard, make sure the slice view has focus (give focus by clicking with the middle mouse button). Then, the o and p keys move one slice forward/backward, respectively. Alternatively, Ctrl+Up and Ctrl+Down accomplish the same. To move in increments of 10 slices, use Ctrl+Shift+Up and Ctrl+Shift+Down.
  • Enlarge a single slice view. Press x, y or z, respectively, to enlarge a single slice view. Another press toggles back to the original layout of showing the three slice views plus the 3D view.