diff --git a/CMakeLists.txt b/CMakeLists.txt
new file mode 100644
index 0000000..eabe14b
--- /dev/null
+++ b/CMakeLists.txt
@@ -0,0 +1,43 @@
+#Specify the version being used aswell as the language
+cmake_minimum_required(VERSION 2.8.11)
+
+#Name your project here
+project(pointmets)
+
+#set the module directory
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}")
+
+#find the STIM library
+find_package(STIM REQUIRED)
+
+#find the approximate nearest neighbor library
+find_package(ANN REQUIRED)
+
+#find the pthreads package
+find_package(Threads)
+
+include_directories(
+					${STIM_INCLUDE_DIRS}
+					${ANN_INCLUDE_DIR}
+					)
+
+#Assign source files to the appropriate variables
+file(GLOB SRC_CPP "*.cpp")
+file(GLOB SRC_H "*.h")
+
+#create an executable file
+add_executable(pointmets
+				${SRC_H} 
+				${SRC_CPP} 
+				)
+
+#set the link libraries
+target_link_libraries(pointmets
+					  ${CMAKE_THREAD_LIBS_INIT} 
+					  ${ANN_LIBRARY}
+		  )
+
+#copy an OBJ test case
+configure_file(data/blue_gt.txt blue_gt.txt COPYONLY)
+configure_file(data/blue_t.txt blue_t.txt COPYONLY)
+configure_file(data/blue_gt.bmp blue_gt.bmp COPYONLY)
\ No newline at end of file
diff --git a/FindANN.cmake b/FindANN.cmake
new file mode 100644
index 0000000..c4b5649
--- /dev/null
+++ b/FindANN.cmake
@@ -0,0 +1,42 @@
+# - Try to find ANN
+# Once done this will define
+#  
+#  ANN_FOUND        - system has ANN
+#  ANN_INCLUDE_DIR  - the ANN include directory
+#  ANN_LIBRARY      - Link these to use ANN
+#   
+
+IF (ANN_INCLUDE_DIRS)
+  # Already in cache, be silent
+  SET(ANN_FIND_QUIETLY TRUE)
+ENDIF (ANN_INCLUDE_DIRS)
+
+FIND_PATH( ANN_INCLUDE_DIR ANN/ANN.h
+           PATHS "/usr/include" "C:/libs/ANN/include")
+
+if( WIN32 )
+
+	set(ANN_LIBRARY $ENV{ANN_PATH}\\ANN.lib)
+	set(ANN_INCLUDE_DIR $ENV{ANN_PATH})
+
+               
+	 # Store the library dir. May be used for linking to dll!
+	 # GET_FILENAME_COMPONENT( ANN_LIBRARY_DIR ${ANN_LIBRARY} PATH )
+
+	 find_package_handle_standard_args(ANN DEFAULT_MSG ANN_INCLUDE_DIR)
+ 
+else (WIN32)
+
+ FIND_LIBRARY( ANN_LIBRARY
+               NAMES ann ANN
+               PATHS /lib /usr/lib /usr/lib64 /usr/local/lib )
+
+endif( WIN32)
+
+
+IF (ANN_INCLUDE_DIR AND ANN_LIBRARY)
+  SET(ANN_FOUND TRUE)
+ELSE (ANN_INCLUDE_DIR AND ANN_LIBRARY)
+  SET( ANN_FOUND FALSE )
+ENDIF (ANN_INCLUDE_DIR AND ANN_LIBRARY)
+
diff --git a/FindSTIM.cmake b/FindSTIM.cmake
new file mode 100644
index 0000000..700157d
--- /dev/null
+++ b/FindSTIM.cmake
@@ -0,0 +1,9 @@
+include(FindPackageHandleStandardArgs)
+
+set(STIM_INCLUDE_DIR $ENV{STIMLIB_PATH})
+
+find_package_handle_standard_args(STIM DEFAULT_MSG STIM_INCLUDE_DIR)
+
+if(STIM_FOUND)
+    set(STIM_INCLUDE_DIRS ${STIM_INCLUDE_DIR})
+endif()
\ No newline at end of file
diff --git a/data/blue_gt.bmp b/data/blue_gt.bmp
new file mode 100644
index 0000000..354a11c
Binary files /dev/null and b/data/blue_gt.bmp differ
diff --git a/data/blue_gt.txt b/data/blue_gt.txt
new file mode 100644
index 0000000..7d0c82e
--- /dev/null
+++ b/data/blue_gt.txt
@@ -0,0 +1,210 @@
+3	686
+19	537
+46	587
+57	785
+73	465
+99	367
+103	657
+109	1038
+115	304
+149	665
+175	984
+187	324
+191	1069
+200	628
+205	566
+218	388
+242	494
+242	633
+249	288
+249	745
+259	442
+270	193
+292	984
+297	539
+297	688
+313	463
+322	342
+329	842
+337	304
+342	407
+380	517
+382	1003
+394	306
+398	372
+400	1071
+401	658
+410	236
+419	585
+421	421
+433	101
+433	182
+433	793
+435	492
+471	341
+474	515
+479	244
+480	1012
+484	310
+485	873
+489	95
+498	174
+501	443
+501	772
+504	388
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+529	239
+531	488
+544	556
+558	411
+561	99
+562	276
+566	728
+574	624
+574	1044
+578	220
+580	146
+586	44
+605	326
+606	385
+611	536
+620	95
+625	692
+636	458
+642	213
+645	578
+650	37
+653	283
+656	735
+659	387
+669	106
+698	528
+700	460
+703	10
+708	1073
+711	382
+713	884
+715	292
+715	667
+721	197
+724	735
+731	233
+736	57
+737	582
+746	638
+748	158
+763	483
+775	706
+777	202
+779	531
+779	950
+787	599
+793	102
+793	322
+794	1074
+797	368
+816	278
+829	478
+831	648
+836	191
+840	730
+847	106
+847	938
+849	559
+850	377
+854	814
+874	676
+875	215
+877	329
+879	174
+896	438
+897	22
+904	868
+906	733
+909	217
+910	265
+918	589
+930	645
+931	143
+937	492
+937	690
+945	824
+947	234
+949	408
+965	310
+970	88
+979	135
+979	450
+979	539
+981	290
+999	213
+999	937
+1003	1007
+1004	380
+1019	832
+1029	183
+1029	312
+1035	744
+1036	68
+1063	556
+1083	165
+1083	423
+1092	729
+1099	11
+1099	344
+1104	241
+1117	106
+1118	827
+1129	666
+1133	485
+1149	19
+1157	152
+1159	570
+1160	410
+1176	325
+1179	244
+1185	702
+1189	778
+1192	472
+1217	559
+1222	202
+1244	95
+1245	310
+1251	255
+1252	142
+1253	422
+1278	474
+1280	567
+1304	177
+1309	710
+1338	329
+1339	255
+1339	413
+1363	555
+1363	678
+1364	489
+1367	180
+1369	107
+1384	774
+1405	339
+1447	624
+1453	426
+1461	133
+1462	357
+1473	853
+1488	500
+1488	766
+1516	642
+1551	484
+1578	837
+1588	331
+1603	741
+1632	628
+1635	367
+1641	472
+1654	566
+1686	924
+1704	819
+1754	694
+1777	785
+1852	381
\ No newline at end of file
diff --git a/data/blue_t.txt b/data/blue_t.txt
new file mode 100644
index 0000000..e6239ab
--- /dev/null
+++ b/data/blue_t.txt
@@ -0,0 +1,214 @@
+2	680
+28	535
+44	588
+57	786
+66	556
+73	463
+100	368
+101	657
+113	1037
+116	303
+148	670
+186	325
+186	985
+191	1075
+193	627
+205	562
+218	387
+220	875
+244	749
+245	631
+246	491
+252	287
+259	444
+274	196
+283	1075
+300	543
+300	980
+302	685
+316	464
+324	340
+332	842
+338	306
+344	408
+381	518
+387	998
+397	371
+398	306
+402	1070
+406	661
+409	237
+419	583
+425	420
+433	182
+434	100
+436	797
+442	494
+472	339
+473	519
+478	246
+479	322
+484	873
+488	1004
+490	94
+498	174
+503	773
+504	442
+507	388
+525	338
+527	243
+535	487
+543	558
+559	416
+561	98
+563	278
+569	731
+573	625
+577	223
+577	1036
+583	145
+586	43
+606	327
+607	387
+611	536
+620	98
+628	690
+634	458
+644	215
+644	582
+648	36
+652	286
+656	740
+660	386
+669	105
+697	531
+700	461
+707	0
+709	1075
+713	381
+715	666
+715	883
+717	295
+724	204
+726	741
+731	230
+737	587
+739	57
+744	157
+744	641
+764	479
+774	950
+778	706
+780	205
+781	531
+790	603
+792	314
+794	104
+795	1075
+798	374
+817	282
+832	478
+832	647
+837	193
+842	731
+846	104
+847	382
+848	814
+851	562
+854	936
+877	213
+878	172
+878	333
+880	674
+897	26
+897	437
+903	220
+906	870
+911	264
+913	737
+918	591
+933	142
+936	494
+936	649
+946	690
+946	821
+947	232
+954	405
+970	89
+970	303
+977	136
+983	542
+985	451
+995	934
+1002	209
+1006	381
+1007	1011
+1024	189
+1025	834
+1029	311
+1031	744
+1035	70
+1064	557
+1082	164
+1083	423
+1094	733
+1099	12
+1101	342
+1105	244
+1116	828
+1120	103
+1123	661
+1130	488
+1149	23
+1156	572
+1157	154
+1161	411
+1176	244
+1177	326
+1187	702
+1195	780
+1196	472
+1219	563
+1221	203
+1242	315
+1244	94
+1250	258
+1251	143
+1253	423
+1277	862
+1281	479
+1283	570
+1302	712
+1306	176
+1336	331
+1338	258
+1338	415
+1363	490
+1365	559
+1365	683
+1367	181
+1369	106
+1384	777
+1401	338
+1404	883
+1436	629
+1452	429
+1462	132
+1464	363
+1474	859
+1481	504
+1485	772
+1516	646
+1550	487
+1578	841
+1585	331
+1601	744
+1629	632
+1636	370
+1639	473
+1649	569
+1683	928
+1699	823
+1750	700
+1771	787
+1848	384
diff --git a/main.cpp b/main.cpp
new file mode 100644
index 0000000..1fffda0
--- /dev/null
+++ b/main.cpp
@@ -0,0 +1,207 @@
+#include <iostream>
+#include <fstream>
+#include <vector>
+#include <string>
+#include <fstream>
+#include <stim/math/vector.h>
+#include <stim/parser/arguments.h>
+#include <stim/parser/filename.h>
+#include <stim/image/image.h>
+#include <ANN/ANN.h>
+
+//load a set of points from an ASCII file
+std::vector< stim::vec<float> > points_from_list(std::string filename){
+
+	std::vector< stim::vec<float> > result;		//create an array to store the result
+
+	std::string str;
+
+	//load the ground truth
+	std::ifstream gfile(filename.c_str());
+	while(std::getline(gfile, str)){
+		stim::vec<float> v(str);
+		result.push_back(v);
+	}
+
+	return result;			//return the list of points
+}
+
+//load a set of points from an image (nonzero values are point positions)
+std::vector< stim::vec<float> > points_from_image(std::string filename){
+
+	stim::image<unsigned char> I;		//create an image object
+
+	I.load(filename);					//load the image file
+
+	std::vector<unsigned long> idx = I.sparse_idx();		//get the 1D indices for each nonzero pixel
+
+	std::vector< stim::vec<float> > result;					//generate an array to store the 2D pixel positions
+	result.resize(idx.size());								//allocate the space to save time
+
+	unsigned long w = I.width();							//get the image width (used to resolve the 2D pixel position from the 1D index)
+
+	unsigned long x, y;
+	for(unsigned long i = 0; i < idx.size(); i++){
+		y = idx[i] / w;
+		x = idx[i] - y * w;
+
+		result[i] = stim::vec<float>(x, y);
+	}
+
+
+	return result;											//return the array of points
+
+}
+
+/// This function calculates the number of hits (
+void calc_hitlist(std::vector< unsigned int >& hits,
+					std::vector< float >& dists,
+				    std::vector< stim::vec<float> > data,
+				    std::vector< stim::vec<float> > query){
+
+	int n_data = data.size();
+	int n_query = query.size();
+
+	//allocate space in the hit lists
+	hits.resize(n_query);
+	dists.resize(n_query);
+
+	//calculate the spatial dimension
+	unsigned int dim = 1;
+	for(unsigned int i = 0; i < data.size(); i++)
+		if(data[i].size() > dim) dim = data[i].size();
+
+										//number of data points
+	ANNpointArray dataPts = annAllocPts(n_data, dim);				//array of data points
+	ANNpoint queryPt = annAllocPt(dim);							//query point
+	ANNidxArray nnIdx = new ANNidx[1];							//indices of nearest neighbors
+	ANNdistArray sq_dist = new ANNdist[1];						//array of squared distances to nearest neighbors
+
+	//load the ground truth points into the ANN point array
+	for(unsigned int i = 0; i < data.size(); i++){
+		for(unsigned int d = 0; d < dim; d++){
+			dataPts[i][d] = data[i][d];
+		}
+	}
+
+	//create a KD-tree
+	ANNkd_tree* kdTree;											//KD tree search structure
+	kdTree = new ANNkd_tree(dataPts, n_data, dim);				//create the KD tree search structure
+
+
+	//submit each query point to the KD tree to find the nearest neighbor
+	for(unsigned int q = 0; q < n_query; q++){
+
+		for(unsigned int d = 0; d < dim; d++){
+			queryPt[d] = query[q][d];
+		}
+
+		//query the KD-tree
+		kdTree->annkSearch(queryPt, 1, nnIdx, sq_dist);
+
+		//put the result in the hit array
+		hits[q] = nnIdx[0];
+		dists[q] = sqrt(sq_dist[0]);
+	}
+}
+
+int main(int argc, char** argv){
+
+	//output advertisement
+	std::cout<<std::endl<<std::endl;
+	std::cout<<"========================================================================="<<std::endl;
+	std::cout<<"Thank you for using the PointMets validation tool!"<<std::endl;
+	std::cout<<"Scalable Tissue Imaging and Modeling (STIM) Lab, University of Houston"<<std::endl;
+	std::cout<<"Developers: David Mayerich"<<std::endl;
+	std::cout<<"Source: https://github.com/stimlab/hsiproc.git"<<std::endl;
+	std::cout<<"========================================================================="<<std::endl<<std::endl;
+
+
+	stim::arglist args;
+
+#ifdef _WIN32
+	args.set_ansi(false);
+#endif
+
+	//add arguments
+	args.add("help", "prints this help");
+	args.add("r", "maximum possible distance to consider a point 'detected'", "10", "[positive value]");
+
+	//parse the command line arguments
+	args.parse(argc, argv);
+
+	//display the help text if requested
+	if(args["help"].is_set()){				
+		std::cout<<std::endl<<"usage: pointmets ground_truth test_case --option [A B C ...]"<<std::endl;
+		std::cout<<std::endl<<std::endl
+				  << "examples: pointmets blue_gt.txt blue_t.txt"<<std::endl;
+		std::cout << "          pointmets blue_gt.bmp blue_t.bmp" << std::endl;
+		std::cout<<std::endl<<std::endl;
+		std::cout<<args.str()<<std::endl;
+		exit(1);
+	}
+
+	//if the input and output files aren't specified, throw an error and exit
+	if(args.nargs() < 2){
+		std::cout<<"ERROR: Two files must be specified for comparison, enter pointmets --help for options."<<std::endl<<std::endl;
+		exit(1);
+	}
+
+	//get the ground truth and test file
+	stim::filename gfilename(args.arg(0));
+	stim::filename tfilename(args.arg(1));
+
+	//set the radius
+	float r = args["r"].as_float();
+
+	std::vector< stim::vec<float> > G;
+	std::vector< stim::vec<float> > T;
+	
+
+	//if an ASCII list of points is specified
+	if(gfilename.get_extension() == "bmp")
+		G = points_from_image(gfilename.str());
+	else
+		G = points_from_list(gfilename.str());
+
+	if(tfilename.get_extension() == "bmp")
+		T = points_from_image(gfilename.str());
+	else
+		T = points_from_list(tfilename.str());
+
+	//calculate the hit list and distances for the test array
+	std::vector< unsigned int > T_hits;
+	std::vector< float > T_dists;
+	calc_hitlist(T_hits, T_dists, G, T);
+
+	//calculate the hit list and distances for the ground truth array
+	std::vector< unsigned int > G_hits;
+	std::vector< float > G_dists;
+	calc_hitlist(G_hits, G_dists, T, G);
+
+	//count up metrics for each test point
+	std::vector< unsigned int > TP;
+	std::vector< unsigned int > FP;
+	unsigned int g, t;
+	for(t = 0; t < T.size(); t++){
+
+		//a true positive has a matching hit in both hit lists, with a distance less than the radius
+		g = T_hits[t];
+		if(G_hits[g] == t && T_dists[t] <= r) TP.push_back(t);
+		else FP.push_back(t);
+	}
+
+	std::vector< unsigned int > FN;
+	for(g = 0; g < G.size(); g++){
+		t = G_hits[g];
+		if(T_hits[t] != g || G_dists[g] > r) FN.push_back(g);
+	}
+
+	std::cout<<"N: "<<G.size()<<std::endl;
+	std::cout<<"TP: "<<TP.size()<<"   ( "<<(double)TP.size() / (double)G.size() * 100<<"% detected)"<<std::endl;
+	std::cout<<"FN: "<<FN.size()<<"   ( "<<(double)FN.size() / (double)G.size() * 100<<"% undetected)"<<std::endl;
+	std::cout<<"FP: "<<FP.size()<<"   ( "<<(double)FP.size() / (double)T.size() * 100<<"% incorrectly detected)"<<std::endl;
+
+
+
+}
--
libgit2 0.21.4