For Labeling circles or spheres,
and measuring nearest neighbor distances.
(The Particle Cluster tool also givis this statistic.) Often
images have circular objects to be measured, but it is difficult to segment
the circles automatically. This tool is
a rapid manual circle tool measurer.
Select the image on which to work. Gray scale or RGB images will work
as of 11/10/03.
Circle On!, Off!,
Turns circle tool on or off. Also turns marked circles on or off.
set tool color Color
of the circle tool. Marked circles have their own color. Clicking,
sets the color of the tool to the color of the Color
turns drawing of tool on and off
turns drawing of circles on and off
turns drawing of labels on and off
all three on (the default condition).
Marks a circle. 1,2,3 are categories or ranks that can have different colors.
Assigns color of that rank to the color of the '***Buttons***
/ Pick Color' button.
Clears all circles for that rank. Click all 3 to clear all circles.
- Circles Plots circles within a range
of radii. Temporary.
A circle is set for each click. Diameter is the diameter of the tool.
Category is 1 unless you change it. For
counting objects of roughly the same diameter. Each click is equivalent
to moving the circle tool, then clicking “Record”.
the list of circles to a text file <image name>-<date &
time>.txt, to the default WRITE
directory. The text file is text, tab
delimited and readable by Excel.
corresponding image must be displayed and selected with 'Image!'. Reads
the file written above, from the default WRITE directory. Displays
the circles on the image if 'Circle On!' is clicked. Note
the circle counts to the right of the clear button. (Images
are read from the default READ directory. This keeps the files separate.
I find this convenient at least.)
the circle lists from two or more text files to one larger text file.
Image names removed.
- Ring Average Plot This is a plot
of averaged intensity around a circle of radius r vs. r.
Sector Average Plot
calculate nearest neighbor
list This is time consuming for large numbers (100's) of circles.
plot c-c nearest neighbor
pairs Plots center to center lines between all nearest neighbors.
Print nn data Prints
center to center distance, edge to edge distance and inclination angle
for the lines between centers of all nearest neighbors (pairs).
These last two work on one or more file without loading the circles.
List CC NN Distances
Prints a collumn of numbers in the Text Output Window. These are the center
to center nearest neighbor distances between the circles in the chosen files,
in the chosen categories. Distances are
List CC NN Distances &
ID Prints the same collumn as above, but with additional collumns with
indices of the circles for that pair, and image names above the corresponding
rows. For identifying specific NN distances
on an image.
How the Nearest Neighbor distances
Each circle is paired with its
nearest neighbor from the categories selected, making a list of
paired circles. Duplicate pairs are removed, eg., (circle 8, circle 10)
is a duplicate of (circle 10, circle 8).
In other words the distance between any two circles is printed only once.
Dragging the center small
circle moves the circle tool, and dragging the outer small circle changes
its diameter. Note the location on the circle can be changed for measuring
circles partly off the edge of the image.
Note that coordinates and
radius of circle tool at the top of the button window.
Using Record and Read above,
work on a large image can be stopped and continued or reviewed at
a later time.
If the circle tool is hard
to see, try a different color. For example if the image aredark,
Orange works well.
- Use the categories for good, questionable and
To view the image without
the overlying circles, click 'Off!'. 'On!' will restore the circlesand
the circle tool in its last position.
To get rid of one circle
in the middle of the list, edit the text file and re-load it.
For large images, view
a part of the image at a time, rather than zooming down, anduse
- To get rid of the circle tool and still show all
marked circles, make the window larger thanthe
image by dragging the border (Mac: size box), drag the circle tool over the
border, then resize the window to the image