Measuring the Area of Irregular Shaped Objects in Digital Images

Measuring the Area of Irregular Shaped Objects in Digital Images
Measuring the Area of Irregular Shaped Objects in Digital Images
Using ImageAnalysis Software
John Pickle, Museum of Science. March 1, 2005
The ImageAnalysis software allows you to measure distances, areas, and color
using a wide variety of digital images, including those taken with a digital
camera, color-coded maps, aerial photographs, and satellite images.
1) Before making any measurements, you must first calibrate the size of a pixel
to a size of an object of known length that is visible in the image. This
procedure automatically starts after you select an image. If you can't calibrate
the pixel size, you will still be able to make relative measurements of the
percentage of pixels of specific colors in selected areas of the image.
There are 2 ways to calibrate the pixel size.
a) Use the "Known Pixel Size" option if you are using satellite images or special
aerial photographs, called orthophotographs, in which the area represented by
each pixel represents the same area on the ground. NOTE: This calibration
option requires that the image you are using is equal to or smaller to the
maximum size the software can use without converting the original to a smaller
image. The image size used in ImageAnalysis is 672 pixels wide by 587 pixels
high.
b) Use the “Scale Present in Image” while working with digital camera images
that have an object of known size in the image. For this latter option:
Click and drag the cursor across the length of the scale – you may adjust
the ends of the line with the small arrows that appear below the image.
TIP: Use the longest length possible since this minimizes small errors of
drawing the calibration line.
In the lower right corner of the window, type the length of the line along
the scale and then type the unit of the scale. Use the small arrows at the
bottom of the window to fine tune the location of the line drawn along
the scale.
TEST YOUR CALIBRATION: After completing the calibration, use the
“line” analysis tool to measure the length of the scale. If possible,
measure a visible scale perpendicular to the direction of the first test.
For example, if you used the length of a ruler to calibrate the pixel size,
use the width of the ruler as the second test, if it is visible.
DISPLAY TOOLS
The next step is to isolate the color of the object you want to measure from the
surrounding objects. The display tools provide enhancements to help quickly
visualize the color characteristics across the entire image. There are 7
automatically calculated enhancements to view the digital image, and these are
very useful as an initial analysis of the image.
1) RGB
2) Red (gray)
3) Green
4) Blue
5) Red v Green 6) Red v Blue 7) Green v Blue
1) Red-Green-Blue (RGB) = standard color composite of digital imagery in
which the color intensities of red, green, and blue are displayed in the
computer display's red, green, and blue, respectively.
2-4) Red, Green, or Blue as shades of gray. A gray shade image of only one of
the images primary colors. Gray shade images allow you to examine the
intensities of values without biasing your sensitivity to red, green, or blue. If
red is being displayed as gray, high intensities appear white, low intensity
appear black.
5-7) Red versus Green, Red versus Blue, or Green versus Blue (normalized):
Provides a comparison of the two color intensities. The displayed color is the
greater of the two intensities. If equal, the displayed color is black. The
difference of the color intensities is divided by the sum of the color intensities.
This provides a way to minimize the effects of shadows and indirect lighting
within the image.
For example, suppose Red vs Green (normalized) is selected. If a pixel has red,
green, and blue (RGB) values of 40%, 80%, and 60%, respectively, the difference
between red and green is 40% in the green, and the sum of the red and green
intensities is 120%. The normalized value will be 40% / 120% or 0.33, which is
converted back to percent values of 33% for display purposes. The displayed
color for that pixel will be a dark shade of green (RGB values of 0%, 33%, 0%).
Compare this value to another pixel with a difference between red and green of
40%, but in this case the pixel has RGB values of 0%, 40%, 20%. The normalized
difference is 40% / (0% + 40%) which equals 1. This value is converted back to
a percentage of 100%. The pixel will be displayed as a very bright green (RGB
value of 0%, 100%, 0%).
To select a tool, click on the box directly beneath the red text "Display Tools".
The list of the eight visualizations will be available. Move the cursor to your
selection and release. The visualization you have selected will appear in the
text of the button and the image will appear in the window.
To see the RGB digital image while viewing a different display, click on the
button 'Show Original Window' and a window with the RGB image will appear.
You may drag this image to any position on the computer screen, and you may
use the point, line, and area on this image as well as the enhanced image
displayed on the larger window.
ANALYSIS TOOLS
All three analysis tools provide color analyses of selected pixels in the image.
The Point Tool shows the intensities of red, green, and blue at any pixel.
Click anywhere on the image and the cross hair will show your location. You
may click again on a point of interest or you may use the arrows on the right of
the picture to move the cross hair. The red, green, and blue components of the
color at the point are automatically output, as are colored boxes of matching
intensities.
The Line Tool shows the average red, green, and blue intensities of pixels
along the selected line.
Click on the image (a blue dot marks the beginning of the line) and drag to a
point of interest (a red dot marks the end of the line). You may change the end
points of the line may be moved with the small arrows along the right edge of
the picture or you may click and drag a new line.
If the pixel size is calibrated, the length of the line is automatically output.
After any calculation, you may save all measurements (point, line, and area) by
using the “Save Measurement” option in the File Menu.
The Area Tool provides the average red, green, and blue intensities of all pixels
within the selected rectangular area.
Click on the image (a blue dot marks the first corner of the box) and drag to a
point of interest (a red dot marks the opposite corner of the box). You may
change the end points of the box may be moved with the small arrows along
the right edge of the picture or you may click and drag a new box.
If the pixel size is calibrated, the area of the box is automatically output. After
any calculation, you may save all measurements (point, line, and area) by using
the “Save Measurement” option in the File Menu.
These color outputs from each of the analysis tools are very useful when
identifying color differences of the object of interest and its background – this
is essential before applying the last of the display tools.
MASK TOOL
The last option of the display tools
is 'Set Range of Colors to Show',
which will be called the Mask Tool
for short. This tool allows you to
highlight pixels of specific color
ranges, and it counts the highlighted
pixels and calculates the area
represented by these pixels.
You may use any of the display
enhancements with the Mask Tool.
To change, click the pop up menu
button labeled “Set Range of Colors
to Show”
To save time in setting the range of
colors, select an analysis tool and
click and/or drag on the object of
interest in the image. The colors of
pixels selected by the tools are
automatically input into the Mask
Tool color ranges. Notice there are
two ranges you may change – the
maximum value and the minimum
value of each color. Use the small
up and down arrows above and
below each graph to change the
color range. To see what parts of the
image fall within the selected color
range, click “Show Colors within
Above Limits”.
TIP: Consider using only one or two
color components to highlight an
object of interest. Either click on the
small color bar graph or click on the
check boxes next to “Selected”.
Only the colors that are checked will
be used to mask the image.
There are two ways to view the highlighted pixels. One is a black and white
image, where the black represents the pixels that met the color thresholds.
The second is a color image where true colors represent the pixels within the
color limits and inverted or distorted colors show the pixels outside the color
ranges. You may also see the image used to create the color “mask”. To
change the display, click the pop up menu button in the lower left of the
window that is just below the text “Visualization of Matching Pixels”.
Notice the output at the bottom of the image. The percent of highlighted pixels
for the entire image is output. If the pixel size is calibrated, the area of the
highlighted pixels is calculated. If the line or area analysis tool is in use,
additional information about the highlighted pixels in relation with the selected
line or area is calculated too.
After you make a color "mask" that has isolated your object of interest, use the
Area Tool to create a box that encloses the object. The area of highlighted
pixels within the rectangle you have drawn is calculated.
Voila, the area of the leaf is 9.07 square inches. Try opening the picture several
times, calibrate, and see if the area of the leaf changes.
If you are working on maps of the same size and location but representing
different periods of time, you will be given the option to keep the calibration of
pixel size and even your color thresholds and area or line locations to save
time.
You may save any of your measurements to a text file by selecting the 'Save
Measurement' option in the File menu.
Quick Reference Guide for Area Measurements with Digital Images
1) Calibrate pixel size when opening the image
a) Known pixel size (image must be smaller than 672 x 587 pixels)
b) Scale present in image
Test you calibration by measuring object of known length in image
2) Using the Display Tools, find the best color enhancement that helps isolate
the object of interest from surrounding features
3) Using either the line or area analysis tool, select pixels within the object to
be measured
4) Select the Mask Tool option from the Display Tools
5) Find the best range of colors that highlight only pixels within the object to be
measured. Highlight the pixels within the selected range of colors.
6) Using the Area Tool, draw a box around the highlighted object of interest.
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