OriginalArticleImprovedDetectionofBranchingPointsinAlgorithmsforAutomatedNeuronTracingfrom3DConfocalImagesYousefAl-Kofahi,1NatalieDowell-Mesfin,2ChristopherPace,2WilliamShain,2JamesN.Turner,2BadrinathRoysam1*Abstract1RensselaerPolytechnicInstitute,Troy,Automatedtracingofneuronalprocessesfrom3Dconfocalmicroscopyimagesisessen-NewYork12180tialforquantitativeneuroanatomyandneuronalassays.Twobasicapproachesare2TheWadsworthCenter,NYStatedescribedintheliterature—onebasedonskeletonizationandanotherbasedonsequen-DepartmentofHealth,Albany,NewYorktialtracingalongneuronalprocesses.Thisarticlepresentsalgorithmsforimprovingthe12201-0509rateofdetection,andtheaccuracyofestimatingthelocationandprocessanglesatbranchingpointsforthelatterclassofalgorithms.TheproblemofsimultaneouslyReceived29December2007;Revisiondetectingbranchpointsandestimatingtheirmeasurementsisformulatedasageneral-Received24August2007;Accepted31izedlikelihoodratiotestdefinedonaspatialneighborhoodofeachcandidatepoint,inOctober2007whichlikelihoodswerecomputedusingaridgedetectionapproach.Theaveragedetec-Thisarticlecontainssupplementarytionrateincreasedfromfrom37to86%.TheaverageerrorinlocatingthebranchmaterialavailableviatheInternetatpointsdecreasedfrom2.6to2.1voxelsin3Dimages.Thegeneralizedhypothesistesthttp://www.interscience.wiley.com/improvestherateofdetectionofbranchingpoints,andtheaccuracyoflocationesti-jpages/1552-4922/suppmat.mates,enablingamorecompleteextractionofneuroanatomyandmoreaccuratecountingofbranchpointsinneuronalassays.Moreaccuratebranchpointmorphome-*Correspondenceto:Prof.Badrinathtryisvaluableforimageregistrationandchangeanalysis.'2007InternationalSocietyforRoysam,JEC7010,RensselaerAnalyticalCytologyPolytechnicInstitute,Troy,NY12180-3590,USAKeytermsEmail:roysam@ecse.rpi.eduautomatedneuritetracing;branchpoints;ridgedetection;generalizedlikelihoodratioPublishedonline7December2007intestWileyInterScience(www.interscience.wiley.com)THEgoalofthisworkistoimproveautomat