How can I measure distances in an images?

Along with counting and measuring objects, measuring the distance between them can be a valuable tool in evaluating their relationships. There are a range of ways in which such measurements can be made, from fully manual to fully automatic.

Like any measurement, it all starts with calibrations. Images are made of pixels and unless you know the distance between pixels in all dimensions, width, height and depth, any measurement will be meaningless. The pixel calibration can be set under Data> Pixel Size... 

Calibration values are usually imported automatically but they can be manually adjusted here if required. Note that the default assumption is that pixels are 1um wide in every dimension, so if the current pixel calibration is still at 1um, it is most likely not correctly calibrated.

If your image is calibrated there are a range of tools that can be used to measure distances:

  • The Measure tool works exclusively in 2D on a single plane. It is very easy to use requiring only that you drag and drop using the cursor to define a distance and the measurement appears on the image as it is drawn.
  • The 3D Polyline tool works similarly but with a few advantages. With a polyline users can make measurements across multiple planes in 3D and the results are automatically added to the Objects table. A 3D polyline is also really easy to define in a Virtual Reality software like arivis VisionVR.
  • The Distances pipeline operation can be used to measure distances between objects automatically. As a pipeline operation it can be configured to automatically measure the distance between every potential pair of Subject and Reference objects. Subjects and references can be any object in a pipeline of either the same or different type. 
  • The Distance Map voxel operation can also be used to measure distances, though the interpretation of the results is a little more complex. A Distance map may be preferable to the distance filter for a variety of reasons. First, unlike the Distance operator, the calculation time is independent of the complexity of object surfaces so it can be much faster when measuring centre-to-surface distances with large complex surfaces and large numbers of subjects. However, the Distance operation can measure distances between objects no matter how far they are from each other, unlike the Distance Map which is limited to a max of 256 pixels. Also, the distance map produces intensity values that correlate to the distance, rather than an actual distance measurement, and therefore requires additional work to convert the values to distances.

Each of those methods has its advantages and inconveniences. With only a handful of objects, manual measurements are faster and easier. Automatic measurements are more reliable and better for measuring multitudes ob objects.