7. The cellViewer interface

The cellViewer is an image viewing interface that allows you to:

Settings are accessed via the cellViewer menus and the following four sub-panels:

7.1. The Navigate menu

The Navigate menu allows you to browse images from different wells and frames within a plate. The keyboard can also be used for navigation:

  • PageUp and PageDown keys are used to move between frames or positions within a well
  • Home and End keys are used to move between wells within a plate
images/Ch7_Navigate.png

7.2. The Analysis menu

The Analysis menu allows you to monitor segmentation output and feature extraction results, via three sub-menus:

  • Configure segmentation
  • Run segmentation
  • Show feature values
images/Ch7_cellViewer.png

Configure segmentation

The supplied default parameter values for segmentation can be used, or you can tune segmentation parameters interactively, as below:

  • [cellViewer]: Analysis>Configure segmentation
  • [Segmentation configure]: Adjust the segmentation parameters (Row) for each channel (Column).
  • [Segmentation configure]: Click "Apply and test configuration" to preview the effects of your changes on segmentation output.
  • [Segmentation configure]: Once you are satisfied with the results, click "Save" to accept the new settings.
  • [Segmentation configure]: Click "Close" to return to the cellViewer window.
images/Ch7_tune-segmentation-parameters.png

Show feature values

Once features have been extracted, you can use the cellViewer to inspect individual cell feature values alongside the original images.

  • [cellViewer]: Analysis>Show feature values
  • [Configure cell labels]: Select the feature of interest and click "OK"
  • [Configure cell labels]: Or click "Browse feature" to select features.
  • [cellViewer]: Move the mouse pointer over the cell of interest
  • [cellViewer]: The cell’s ID and selected feature value will be shown in the bar at the lower-left of the window.
images/Ch7_show-feature-values.png
images/Ch7_configure-cell-labels.png
images/Ch7_show-feature-values-2.png

7.3. The View menu

The View menu is used to adjust how images will be displayed on the screen. Three types of settings are available:

  • View: Change the well display mode
  • Zoom level: Adjust image view magnification
  • Display: Show single or multiple images
images/Ch7_view.png

View mode

By setting the View mode, you can choose to view the the image frames in a well one at a time or all together.

  • The Single frame mode displays a single image frame in the cellViewer window
  • The Whole well mode displays a grid with all the image frames from the current well.

    • [cellViewer]: View>View mode>Whole well
images/Ch7_view-mode.png

Zoom level

The Zoom option is used to adjust the viewing magnification of images. Six different zoom levels are provided:

  • 25 %
  • 50 %
  • 100 %
  • 200 %
  • 400 %
  • Fit window (adjusts the image to fit the cellViewer window)

    • [cellViewer]: View>Zoom>Fit window
images/Ch7_zoom.png

Display mode

In addition to the default Single display mode, the cellViewer can also display two different images side by side, making it convenient to compare images.

  • Dual display (Vertical) mode displays the images in two separate frames, one above the other.
  • Dual display (Horizontal) mode displays the images in two frames, side by side.

    • [cellViewer]: View>Display mode>Dual display (horizontal)
    • [cellViewer]: Click to select a frame and use the HOME/END/PageUp/PageDown keys to navigate between frames and wells, as in Single display mode.
images/Ch7_display-mode.png