This is a fast-track guide to performing a batch analysis on an image. Pictured is a 30" black shoelace laid onto a whiteboard with scalebars drawn by hand in inches.

Thumbnails are initially presented for faster viewing. You may click on any of the images to see larger versions.

Original 32-Bit Color Image

Original 32-Bit Color Image

Run ImageJ. Now, File > Open... and select your image.

The pictured shoelace measured 31.25 inches long and approximately 3/32 of an inch in diameter.

My calculations show that approximately 54 pixels horizontally is equal to 1 inch, whereas 53 pixels vertically equals 1 inch. The aspect ratio is approximately 1 to 1 (square pixels). By these measurements, the total viewing area is approximately 18.96 inches by 14.49 inches.

End User Settings Dialogue - Batch Customization

End User Settings - Batch Customization

Customize the batch process by Plugins > VNT > Create Settings, which will alter the behavior for all the images in the folder.

By using the ImageJ line selection tool, the number of pixels per inch can be computed, as well as the aspect ratio.

If the automated segmentation proves insufficient, make sure "Keep Temporary Image Files" is checked. This allows for later modification, shown later.

Visual Overlay - Initial Batch Result

Visual Overlay - Initial Batch Result

With your settings file created, the image is ready to be batched. Since we are only analyzing a single image, run Plugins > VNT > Batch File.

New Segmentation - Human Modification

New Segmentation - Human Modification

Assuming we aren't happy with the result, we can change the settings file to change the lighting correction, segmentation routine, or pruning algorithm.

If no segmentation routine is correct for your image (segmentation is hard), check on "(Human Modification) Begin with Segmentation?" This allows you to specify your own binary segmented image.

ImageJ is not a drawing program. Binary images can be created through various ImageJ operations and modified in the GIMP or any other drawing program if necessary.

The pictured segmented image was created by the following:

Eyecandy - Original Image with Quantifying Visual Overlays

Batch Result

After rerunning the batch process by running Plugins > VNT > Batch File on our new segmented image created above, new results are computed. Pictured is the new visualization generated after using the above segmented image. Clearly the analysis depends heavily on the preprocessing.

The tool yielded a length measurement of 31.289 inches. The thickness was measured to be an average of 0.053 inches.

Website and Vascular Network Toolkit for ImageJ are Copyright 2005 - 2012. VNT for ImageJ is an open source toolkit released under the GNU General Public License.