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

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

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.

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.

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

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

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

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.