Re: Measure Distance Between an Array of Points?

Posted by Marcel on Dec 16, 2010; 8:58am
URL: http://imagej.273.s1.nabble.com/Measure-Distance-Between-an-Array-of-Points-tp3686161p3686164.html

Yes you can define your template as a selection in ImageJ (bonus point 1) and and then add this selection to the ROI Manager of ImageJ.

With the ROI-Manager you can a kind of record your selections and then later restore them from the list of the ROI-Manager. ImageJ offers several selection tools for a predefined shape in the Edit->Selection menu.

For the measurements of interpoint distances it is easy to use ImageJ in combination with R.

http://www.r-project.org/

The software Bio7 (sorry for this self-advertisment) offers interfaces between ImageJ and R and offers some methods to transfer ImageJ selections and images to R.
It is available for the OS Windows and Linux.

http://129.70.40.49/modelling/?page_id=75

In addition Bio7 has integrated some functionality to transfer single selections (the point coordinates as vectors) and multiple selections (from the ROI Manager as 2d lists) directly to the R workspace.

If the R package (plugin) "spatstat" is installed you can use the methods nndist (nearest neighbour distances) or pairdist (distances between all pairs of points in a point pattern) to analyze your shapes and also do easily summary statistics and more.

http://www.spatstat.org/

I integrated this functionality in Bio7 to support morphometrics for plants and animals.
For more Morphometrics with R have also a look into this book:
http://www.springer.com/statistics/life+sciences,+medicine+%26+health/book/978-0-387-77789-4