Image Pixel Intensities

As you move the mouse pointer over the image, the slice number, position within the slice, and pixel intensity are shown at the bottom of the Image Display frame. See dimension display.

You can show statistics about the image in the Image Statistics window. Click on Image Stats under the View menu:

view_stats

This brings up the Image Statistics frame, as shown below:

image_stats

The Image Statistics frame shows:

  • A histogram of pixel intensities. If the image has a selected slice, then the histogram is for all pixels in the selected slice, otherwise it is for the pixels in whole the image.
    Note: The histogram intensity range shown on the x-axis reflects the intensity range selected by the contrast-adjustment sliders. As you alter the image contrast, the histogram is adjusted to show intensities only within the displayed max/min intensity range.
  • The slice number for which statistics are shown. If the image does not have a selected slice, then the text "None selected" appears.
  • The number of pixels in the image (or the selected slice) that have a non-zero intensity.
    Note: The number shown is for all non-zero intensity pixels, not just for the pixels within the max/min intensity range.
  • The volume of pixels in the image (or the selected slice) that have a non-zero intensity. If the slice is planar (i.e., the slice thickness is not defined) then the text "N/A" appears.
    Note: The volume shown is for all non-zero intensity pixels, not just for the pixels within the max/min intensity range.
  • The mean intensity of pixels in the image (or in the selected slice).
    Note: The mean shown is for all pixels, not just for the pixels within the max/min intensity range (but excluding pixels with zero intensity from the calculation).

If you select the show_normalised check-box, then the number of pixels on the y-axis is normalised so that the sum of all histogram y-values is equal to 1.0. If you select the exclude_background check-box, then all intensities that are zero-valued will not be included in the histogram; more specifically, the histogram bin that includes the zero value will not be included in the histogram.

As the mouse is moved over the histogram graph, the intensity and number of pixels at the mouse location are shown at the bottom of the Image Statistics frame.

As the mouse is moved over the image, the intensity beneath the mouse is shown as an orange vertical line on the histogram.

image_stats_marker

Note: the colours used in this and other graphs are customisable.

For movies, the Image statistics for the visible slice is continuously updated as the movie steps through the frames.

Writing the Statistics to File

To write the image statistics to a file, choose Write under the File menu in the Image Statistics frame: file_write

The image statistics file shows the number and volume of non-zero intensity image pixels in the loaded image or in the selected slice of the loaded image (if slice selected). If the image is not slice-selected, the number and volume of non-zero intensity image pixels (slice-by-slice) will also be shown in 3 columns. The three columns are the slice number, the number of non-zero pixels in that slice and the volume of non-zero pixels in that slice (in cubic mm). This is followed by the mean pixel intensity and the intensity histogram that is shown in the dialog.

An example of the format of the image statistics written to disk is shown below:

# Image stats written on "15 Dec 2026 13:24:35.321 British Summer Time" by Operator ID "xinapse"
# Build version="8.0_1"
# Image source= "/home/xinapse/images/A.PATIENT._001_STUDY_1_SERIES_6"
# Slice: None selected
# Number of non-zero pixels: 24821
# Volume of non-zero pixels: 2367.115 cu mm
# Slice n-non-zero vol-non-zero
1      6876     655.746459
2      4870     464.439392
3      2637     251.483917
4      2418     230.598449
5      2717     259.113311
6      2091     199.413299
7      1253     119.495391
8      760      72.479248
9      432      41.198730
10     305      29.087066
11     249      23.746490
12     66       6.2942504
13     147      14.019012
&
# Mean pixel intensity: 13342.382821
# Visible histogram:
118.0   0.0
119.0   0.0
120.0   0.0
...

The data intensity histogram is written in a tab-separated table with two columns: the first is the pixel intensity value, and the second is the number of pixels with that intensity. For normalised histograms, the sum of all the values in the second column is equal to 1.0.

Creating a Screen Shot of the Graph

To create a screen shot of the graph, select Create a screen shot of a graph, then, in the next dialog, select the image file format you want.

Creating a PDF File of the Graph

To write the image statistics histogram to a PDF, choose Export as PDF under the File menu in the Image Statistics frame: file_export_pdf

A File Chooser will now pop up for you to select a PDF file to write the histogram and intensity statistics.

Click the done_button button when you have finished with image statistics.