Dear List Members, I'm presently carrying out morphological analysis of a data set of neuronal structures. These are essentially 3D binary trees. In due course I will be trying to use discriminant analysis or other methods to classify these neurons based on morphological variables such as total tree length, segment number etc. I would like to calculate a 3D convex hull for a set of X,Y,Z data points which define the tips of my neurons. I have found the R function chull which finds a 2D convex hull, but not have found any 3D routines. I wondered if there were any packages / publicly available code I could use. Having found the convex hull, it would be handy if there were also functions to find the centroid, volume etc. I've only been using R for 10 days and am not much of a programmer, so I would rather not have to write code to interface to external C routines etc if possible. Very many thanks for any suggestions, Greg. P.S. I'm running R 1.3.1 on MacOS 9.1 __________________________________________________________________________ Greg Jefferis, Lab Address: Liqun Luo, Herrin 144 Neurosciences PhD Programme & e-mail: jefferis at stanford.edu Dept Biological Sciences, Lab: (650) 725 5809 Gilbert Biology Building, Fax: (650) 723 0589 371 Serra Mall, Stanford, CA 94305-5020. Home: (650) 497 1135 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
Finding a 3D convex hull in R
2 messages · Dr Gregory Jefferis, Brian Ripley
On Fri, 21 Sep 2001, Greg Jefferis wrote:
Dear List Members, I'm presently carrying out morphological analysis of a data set of neuronal structures. These are essentially 3D binary trees. In due course I will be trying to use discriminant analysis or other methods to classify these neurons based on morphological variables such as total tree length, segment number etc. I would like to calculate a 3D convex hull for a set of X,Y,Z data points which define the tips of my neurons. I have found the R function chull which finds a 2D convex hull, but not have found any 3D routines. I wondered if there were any packages / publicly available code I could use. Having found the convex hull, it would be handy if there were also functions to find the centroid, volume etc. I've only been using R for 10 days and am not much of a programmer, so I would rather not have to write code to interface to external C routines etc if possible.
3D convex hull programs are very much more specialized than 2D ones. When I added chull I looked at the possibility of allowing kD, k > 2, but it was hard to find suitable code, let alone interface to it. Known algorithms are far too complicated to implement tolerably at R level. netlib.bell-labs.com/netlib/voronoi/hull.html is one place I considered starting, but note the portability comments.
Very many thanks for any suggestions, Greg. P.S. I'm running R 1.3.1 on MacOS 9.1
__________________________________________________________________________ Greg Jefferis, Lab Address: Liqun Luo, Herrin 144 Neurosciences PhD Programme & e-mail: jefferis at stanford.edu Dept Biological Sciences, Lab: (650) 725 5809 Gilbert Biology Building, Fax: (650) 723 0589 371 Serra Mall, Stanford, CA 94305-5020. Home: (650) 497 1135 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272860 (secr) Oxford OX1 3TG, UK Fax: +44 1865 272595 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._