How To Use The Image Tools

Right-clicking in an image displayed in a window will bring up a pop-up menu with the following options:

  • Open image in new window: Displays the image in a new display window. This is useful for getting a closer look at a window subplot that has a small image.

  • Show image histogram: Produces a new window containing a histogram of the pixel intensities in the image. This is useful for qualitatively examining whether a threshold value determined by IdentifyPrimaryObjects seems reasonable, for example. Image intensities in CellProfiler typically range from zero (dark) to one (bright). If you have an RGB image, the histogram shows the intensity values for all three channels combined, even if one or more channels is turned off for viewing.

  • Image contrast: Presents three options for displaying the color/intensity values in the images:

    • Raw: Shows the image using the full colormap range permissible for the image type. For example, for a 16-bit image, the pixel data will be shown using 0 as black and 65535 as white. However, if the actual pixel intensities span only a portion of the image intensity range, this may render the image unviewable. For example, if a 16-bit image only contains 12 bits of data, the resulting image will be entirely black.
    • Normalized (default): Shows the image with the colormap “autoscaled” to the maximum and minimum pixel intensity values; the minimum value is black and the maximum value is white.
    • Log normalized: Same as Normalized except that the color values are then log transformed. This is useful for when the pixel intensity spans a wide range of values but the standard deviation is small (e.g., the majority of the interesting information is located at the dim values). Using this option increases the effective contrast.
  • Interpolation: Presents three options for displaying the resolution in the images. This is useful for specifying the amount of detail that you want to be visible if you zoom in:

    • Nearest neighbor: Use the intensity of the nearest image pixel when displaying screen pixels at sub-pixel resolution. This produces a blocky image, but the image accurately reflects the data.
    • Linear: Use the weighted average of the four nearest image pixels when displaying screen pixels at sub-pixel resolution. This produces a smoother, more visually-appealing image, but makes it more difficult to find pixel borders.
    • Cubic: Perform a bicubic interpolation of the nearby image pixels when displaying screen pixels at sub-pixel resolution. This produces the most visually-appealing image but is the least faithful to the image pixel values.
  • Save subplot: Save the clicked subplot as an image file. If there is only one p lot in the figure, this option will save that one.

  • Channels: For color images only. You can show any combination of the red, green, and blue color channels.