Circle Tool Buttons

04/15/2004

Circle Tool

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.

Buttons

Image 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.
- If the circle tool does not appear with 'On!', if is out of the field of view (where it was in the last image). Press 'Reset!'.
Cookie Cutter
- Reset! Moves circle tool to middle of image. Handy when working on large image that is only partly in view, and the circle tool has been scrolled out of view. Does not erase the circle list - no data is lost.
Display
- 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 menu.
- Toggle tool turns drawing of tool on and off
- Toggle circles turns drawing of circles on and off
- Toggle labels turns drawing of labels on and off
- Reset turns all three on (the default condition).
Record 1,2,3 Marks a circle. 1,2,3 are categories or ranks that can have different colors.
Color 1,2,3 Assigns color of that rank to the color of the '***Buttons*** / Pick Color' button.
Clear 1,2,3 Clears all circles for that rank. Click all 3 to clear all circles.
Plots
- Circles Plots circles within a range of radii. Temporary.
Select
- set rect to cirle New 2/02. Sets the image rectangle (see Select menu) to the
- square centered on and just circumscribing the circle.
Quick Count 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”.
File
- Record Writes 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.
- Load The 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.)
- Concatenate Copy the circle lists from two or more text files to one larger text file. Image names removed.
Analysis
- Ring Average Plot This is a plot of averaged intensity around a circle of radius r vs. r.
  - For circularly symmetric images, or getting averaged intensities from power spectra. To print the plot values, use the Plot / Nav menu.
- Sector Average Plot
  - Plots sector average profile. Average along radius (in thin sector) with angle theta, vs. theta. Angular width of sector is 1 degree.
Stats
- 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 in pixels.
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 are measured.

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.

Hints

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 other objects.
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 the navigator.
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 size.