diff --git a/cells_small.json b/cells_small.json
new file mode 100644
index 0000000000000000000000000000000000000000..01dc71bd84eb623c4a682d45e9665732d36ad57e
--- /dev/null
+++ b/cells_small.json
@@ -0,0 +1,1261 @@
+[{
+ "mechanisms": [{
+  "indexes": [1,11,17],
+  "name": "Ca"
+ },{
+  "indexes": [1,11,17],
+  "name": "CaDynamics_E2"
+ },{
+  "indexes": [1,11,17],
+  "name": "Ca_LVAst"
+ },{
+  "indexes": [1,1,1],
+  "name": "IClamp"
+ },{
+  "indexes": [3,5,6,7,9,13,15,19,21,23,24,25,27,28,29,30,31,32,33,35,36,37,38,39,41,43,45,47,49,50,51,53,54,55,57,58,59,60,61,63,64,65,67,68,69,71,73],
+  "name": "Ih"
+ },{
+  "indexes": [1,3,5,6,7,9,11,13,15,17,19,21,23,24,25,27,28,29,30,31,32,33,35,36,37,38,39,41,43,45,47,49,50,51,53,54,55,57,58,59,60,61,63,64,65,67,68,69,71,73],
+  "name": "Im"
+ },{
+  "indexes": [1,3,5,6,7,9,11,13,15,17,19,21,23,24,25,27,28,29,30,31,32,33,35,36,37,38,39,41,43,45,47,49,50,51,53,54,55,57,58,59,60,61,63,64,65,67,68,69,71,73],
+  "name": "K_Pst"
+ },{
+  "indexes": [1,3,5,6,7,9,11,13,15,17,19,21,23,24,25,27,28,29,30,31,32,33,35,36,37,38,39,41,43,45,47,49,50,51,53,54,55,57,58,59,60,61,63,64,65,67,68,69,71,73],
+  "name": "K_Tst"
+ },{
+  "indexes": [11,17],
+  "name": "NaTa_t"
+ },{
+  "indexes": [1,3,5,6,7,9,13,15,19,21,23,24,25,27,28,29,30,31,32,33,35,36,37,38,39,41,43,45,47,49,50,51,53,54,55,57,58,59,60,61,63,64,65,67,68,69,71,73],
+  "name": "NaTs2_t"
+ },{
+  "indexes": [1,3,5,6,7,9,11,13,15,17,19,21,23,24,25,27,28,29,30,31,32,33,35,36,37,38,39,41,43,45,47,49,50,51,53,54,55,57,58,59,60,61,63,64,65,67,68,69,71,73],
+  "name": "Nap_Et2"
+ },{
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+  "name": "ProbAMPANMDA_EMS"
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+  "name": "ProbGABAAB_EMS"
+ },{
+  "indexes": [1,11,17],
+  "name": "SK_E2"
+ },{
+  "indexes": [1,3,5,6,7,9,11,13,15,17,19,21,23,24,25,27,28,29,30,31,32,33,35,36,37,38,39,41,43,45,47,49,50,51,53,54,55,57,58,59,60,61,63,64,65,67,68,69,71,73],
+  "name": "SKv3_1"
+ },{
+  "indexes": [1,11,17],
+  "name": "ca_ion"
+ },{
+  "indexes": [1,3,5,6,7,9,11,13,15,17,19,21,23,24,25,27,28,29,30,31,32,33,35,36,37,38,39,41,43,45,47,49,50,51,53,54,55,57,58,59,60,61,63,64,65,67,68,69,71,73],
+  "name": "capacitance"
+ },{
+  "indexes": [1,3,5,6,7,9,11,13,15,17,19,21,23,24,25,27,28,29,30,31,32,33,35,36,37,38,39,41,43,45,47,49,50,51,53,54,55,57,58,59,60,61,63,64,65,67,68,69,71,73],
+  "name": "k_ion"
+ },{
+  "indexes": [1,3,5,6,7,9,11,13,15,17,19,21,23,24,25,27,28,29,30,31,32,33,35,36,37,38,39,41,43,45,47,49,50,51,53,54,55,57,58,59,60,61,63,64,65,67,68,69,71,73],
+  "name": "na_ion"
+ },{
+  "indexes": [1,3,5,6,7,9,11,13,15,17,19,21,23,24,25,27,28,29,30,31,32,33,35,36,37,38,39,41,43,45,47,49,50,51,53,54,55,57,58,59,60,61,63,64,65,67,68,69,71,73],
+  "name": "pas"
+ }],
+ "parent_index": [0,0,1,0,3,0,5,6,7,0,9,2,11,10,13,10,15,12,17,14,19,14,21,16,23,24,25,16,27,28,29,30,31,32,33,20,35,36,37,38,39,20,41,26,43,26,45,42,47,42,49,50,51,48,53,54,55,48,57,58,59,60,61,62,63,64,65,62,67,68,69,70,71,70,73]
+},{
+ "mechanisms": [{
+  "indexes": [1,11,17],
+  "name": "Ca"
+ },{
+  "indexes": [1,11,17],
+  "name": "CaDynamics_E2"
+ },{
+  "indexes": [1,11,17],
+  "name": "Ca_LVAst"
+ },{
+  "indexes": [1],
+  "name": "IClamp"
+ },{
+  "indexes": [3,5,6,7,9,13,15,19,21,23,24,25,27,28,29,30,31,32,33,35,36,37,38,39,41,43,45,47,49,50,51,53,54,55,57,58,59,60,61,63,64,65,67,68,69,71,73],
+  "name": "Ih"
+ },{
+  "indexes": [1,3,5,6,7,9,11,13,15,17,19,21,23,24,25,27,28,29,30,31,32,33,35,36,37,38,39,41,43,45,47,49,50,51,53,54,55,57,58,59,60,61,63,64,65,67,68,69,71,73],
+  "name": "Im"
+ },{
+  "indexes": [1,3,5,6,7,9,11,13,15,17,19,21,23,24,25,27,28,29,30,31,32,33,35,36,37,38,39,41,43,45,47,49,50,51,53,54,55,57,58,59,60,61,63,64,65,67,68,69,71,73],
+  "name": "K_Pst"
+ },{
+  "indexes": [1,3,5,6,7,9,11,13,15,17,19,21,23,24,25,27,28,29,30,31,32,33,35,36,37,38,39,41,43,45,47,49,50,51,53,54,55,57,58,59,60,61,63,64,65,67,68,69,71,73],
+  "name": "K_Tst"
+ },{
+  "indexes": [11,17],
+  "name": "NaTa_t"
+ },{
+  "indexes": [1,3,5,6,7,9,13,15,19,21,23,24,25,27,28,29,30,31,32,33,35,36,37,38,39,41,43,45,47,49,50,51,53,54,55,57,58,59,60,61,63,64,65,67,68,69,71,73],
+  "name": "NaTs2_t"
+ },{
+  "indexes": [1,3,5,6,7,9,11,13,15,17,19,21,23,24,25,27,28,29,30,31,32,33,35,36,37,38,39,41,43,45,47,49,50,51,53,54,55,57,58,59,60,61,63,64,65,67,68,69,71,73],
+  "name": "Nap_Et2"
+ },{
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+  "name": "ProbGABAAB_EMS"
+ },{
+  "indexes": [1,23,59],
+  "name": "SK_E2"
+ },{
+  "indexes": [1,3,23,25,26,27,29,59,61,62,63,65,67,68,69,70,71,73,111,113,173,174,175,176,177,179,180,181,183,185,186,187,188,189,249,250,251,253,254,255,256,257,258,259,261,262,263,264,265,267,268,269,270,271,272,273,274,275,293,294,295,296,297,299,300,301,315,316,317,318,319,321,323,325,326,327,329,331,332,333,335,336,337,338,339,340,341,343,344,345,346,347,348,349,351,352,353,355,356,357,359,360,361,363],
+  "name": "SKv3_1"
+ },{
+  "indexes": [1,23,59],
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+  "name": "ProbGABAAB_EMS"
+ },{
+  "indexes": [1,23,59],
+  "name": "SK_E2"
+ },{
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+  "name": "SKv3_1"
+ },{
+  "indexes": [1,23,59],
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+  "name": "ProbGABAAB_EMS"
+ },{
+  "indexes": [1,23,59],
+  "name": "SK_E2"
+ },{
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+  "name": "SKv3_1"
+ },{
+  "indexes": [1,23,59],
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+  "name": "ProbGABAAB_EMS"
+ },{
+  "indexes": [1,23,59],
+  "name": "SK_E2"
+ },{
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+  "name": "SKv3_1"
+ },{
+  "indexes": [1,23,59],
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139,139,139,139,139,139,139,139,139,139,140,140,140,140,141,141,141,141,141,141,141,141,141,141,141,141,141,141,141,141,141,142,142,142,142,142,142,142,142,142,142,142,142,143,143,143,143,145,145,145,145,145,145,145,145,145,145,145,145,145,145,145,145,145,145,145,145,145,145,145,145,145,145,145,145,147,147,147,147,147,147,147,147,147,147,147,147,147,147,147,147,147,147,147,147,147,147,147,147,148,148,148,148,148,148,148,148,148,148,148,148,148,148,148,148,148,149,149,149,149,149,149,149,149,150,150,150,150,150,150,150,150,150,150,151,151,151,151,151,151,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,154,154,154,154,154,154,154,154,154,154,154,154,154,154,154,154,154,154,154,154,154,154,154,154,154,154,154,154,154,154,154,154,154,154,155,155,155,155,155,155,155,155,155,155,155,155,155,155,155,155,155,155,155,155,155,157,159,159,159,159,159,159,159,159,159,159,159,159,159,159,159,159,159,159,159,159,159,159,159,159,159,159,159,159,159,159,159,159,159,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,161,161,161,161,161,161,161,161,161,161,161,161,161,161,161,163,163,163,163,163,163,163,163,163,163,163,163,163,163,163,163,163,163,163,163,163,163,163,163,163,163,163,163,163,163,163,163,163,163,163,163,163,164,164,164,164,164,164,164,164,164,164,164,164,164,164,164,164,164,164,164,164,164,165,165,165,165,165,165,165,165,165,165,165,165,165,165,165,165,165,165,165,165,165,165,166,166,166,166,166,166,166,166,166,166,166,166,166,166,166,166,166,166,166,166,166,166,166,166,166,166,166,166,166,166,166,167,167,167,167,167,167,167,167,167,167,167,167,167,167,167,167,167,167,167,167,168,168,168,168,168,168,168,168,168,168,168,168,168,168,168,168,168,168,168,168,168,168,168,169,169,169,169,169,169,169,169,169,169,169,169,169,169,169,169,169,169,169,169,170,170,170,170,170,170,170,170,170,170,170,170,170,170,170,170,170,170,170,170,170,170,170,171,171,171,171,171,171,171,171,171,171,171,171,171,171,171,171,173,173,173,173,173,173,173,173,173,173,173,173,173,173,173,173,173,173,173,173,173,173,173,173,173,173,174,174,174,174,174,174,174,174,174,174,174,174,174,174,174,174,174,174,174,174,174,174,175,175,175,175,175,175,175,175,175,177,177,178,178,178,178,178,178,178,178,178,178,178,178,178,178,178,178,178,178,178,178,178,178,178,179,179,179,179,179,179,179,179,179,179,180,180,181,181,181,181,181,181,181,181,181,181,183,183,183,183,183,183,183,183,183,183,183,183,183,183,183,183,183,183,183,183,183,184,184,184,184,184,184,184,184,184,184,184,184,184,184,185,185,185,185,185,186,186,186,186,186,186,186,186,186,186,186,186,186,187,187,187,187,187,189,189,189,189,189,189,189,189,189,189,189,189,189,190,190,190,190,190,190,190,190,190,190,190,190,191,191,191,191,191,191,191,193,193,193,193,193,193,193,193,193,193,193,193,193,193,193,194,194,194,194,194,194,194,194,194,194,194,194,195,195,195,195,195,195,195,195,195,195,195,195,195,197,197,197,197,197,197,197,197,197,197,197,197,197,197,198,198,198,198,198,198,198,198,198,198,199,199,199,199,199,199,199,200,200,200,200,200,200,200,200,200,200,200,200,200,200,200,200,200,201,201,201,201,201,201,201,201,201,201,201,201,201,201,201,201,201,201,201,202,202,202,202,202,202,202,202,202,202,202,202,202,202,203,203,203,203,203,203,203,203,203,204,204,204,204,204,204,204,204,204,204,204,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,206,206,206,206,206,206,206,206,206,206,206,206,207,207,207,207,207,207,207,207,207,207,207,207,207,207,208,208,208,208,208,208,208,208,208,208,208,208,208,208,208,208,208,208,209,209,209,209,209,209,209,209,209,209,209,209,209,209,209,209,209,209,209,209,209,210,210,210,210,210,210,210,210,210,210,210,210,210,210,210,210,210,211,211,211,211,211,211,211,211,211,211,211,211,211,212,212,212,212,212,212,212,212,212,212,212,212,212,212,212,212,212,213,213,213,213,213,213,213,213,213,213,213,213,213,213,213,213,213,213,213,213,213,213,213,214,214,214,214,214,214,214,214,214,214,214,214,214,214,214,214,214,214,214,214,214,214,214,214,214,214,214,214,214,214,214,214,214,214,214,214,214,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,215,217,217,217,217,217,218,218,219,219,219,219,219,219,219,219,221,221,221,221,221,221,221,221,221,221,221,221,221,221,221,221,221,221,221,221,221,221,221,221,221,222,222,222,222,222,222,222,222,222,222,222,222,222,222,222,222,222,222,222,222,222,223,223,223,223,223,223,223,223,223,223,223,223,223,223,223,223,223,223,223,223,223,223,225,225,225,225,225,225,225,225,225,225,225,225,225,225,225,225,226,226,226,226,226,226,226,226,226,226,226,226,226,226,226,227,227,227,227,227,227,227,227,227,227,227,227,227,227,227,227,227,228,228,228,228,228,228,228,229,229,229,229,229,229,229,229,229,229,229,231,231,231,231,231,231,231,231,231,233,233,233,233,233,233,233,233,233,233,233,233,233,233,233,233,233,233,233,233,233,233,233,233,233,233,233,233,233,233,233,233,234,234,234,234,234,234,234,234,234,234,234,234,234,234,234,234,234,234,234,234,234,234,234,234,235,235,235,235,235,235,235,235,235,235,235,235,235,235,235,235,235,235,235,235,237,237,237,237,237,238,238,238,238,238,239,239,239,241,241,241,241,241,241,241,241,241,241,241,241,241,242,243,243,243,245,245,245,245,245,245,245,245,245,245,245,245,245,245,245,245,245,245,245,245,245,245,245,245,245,245,245,245,245,247,249,249,249,249,249,249],
+  "name": "ProbGABAAB_EMS"
+ },{
+  "indexes": [1,19,57],
+  "name": "SK_E2"
+ },{
+  "indexes": [1,3,19,21,23,57,59,61,63,64,65,66,67,69,70,71,131,133,134,135,137,138,139,140,141,142,143,145,163,164,165,166,167,168,169,170,171,173,174,175,177,178,179,180,181,183,184,185,186,187,189,190,191,193,194,195,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,219,221,222,223,225,226,227,228,229,231,233,234,235,237,238,239,241,243,245,247,249],
+  "name": "SKv3_1"
+ },{
+  "indexes": [1,19,57],
+  "name": "ca_ion"
+ },{
+  "indexes": [1,3,5,7,9,11,12,13,14,15,17,19,21,23,25,26,27,28,29,31,32,33,34,35,37,39,40,41,43,45,46,47,48,49,50,51,53,55,57,59,61,63,64,65,66,67,69,70,71,73,75,77,79,81,83,84,85,87,89,91,92,93,94,95,97,98,99,100,101,103,105,107,108,109,110,111,113,114,115,116,117,119,120,121,122,123,125,126,127,128,129,131,133,134,135,137,138,139,140,141,142,143,145,147,148,149,150,151,153,154,155,157,159,160,161,163,164,165,166,167,168,169,170,171,173,174,175,177,178,179,180,181,183,184,185,186,187,189,190,191,193,194,195,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,219,221,222,223,225,226,227,228,229,231,233,234,235,237,238,239,241,243,245,247,249],
+  "name": "capacitance"
+ },{
+  "indexes": [1,3,19,21,23,57,59,61,63,64,65,66,67,69,70,71,131,133,134,135,137,138,139,140,141,142,143,145,163,164,165,166,167,168,169,170,171,173,174,175,177,178,179,180,181,183,184,185,186,187,189,190,191,193,194,195,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,219,221,222,223,225,226,227,228,229,231,233,234,235,237,238,239,241,243,245,247,249],
+  "name": "k_ion"
+ },{
+  "indexes": [1,3,19,21,23,57,59,61,63,64,65,66,67,69,70,71,131,133,134,135,137,138,139,140,141,142,143,145,163,164,165,166,167,168,169,170,171,173,174,175,177,178,179,180,181,183,184,185,186,187,189,190,191,193,194,195,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,219,221,222,223,225,226,227,228,229,231,233,234,235,237,238,239,241,243,245,247,249],
+  "name": "na_ion"
+ },{
+  "indexes": [1,3,5,7,9,11,12,13,14,15,17,19,21,23,25,26,27,28,29,31,32,33,34,35,37,39,40,41,43,45,46,47,48,49,50,51,53,55,57,59,61,63,64,65,66,67,69,70,71,73,75,77,79,81,83,84,85,87,89,91,92,93,94,95,97,98,99,100,101,103,105,107,108,109,110,111,113,114,115,116,117,119,120,121,122,123,125,126,127,128,129,131,133,134,135,137,138,139,140,141,142,143,145,147,148,149,150,151,153,154,155,157,159,160,161,163,164,165,166,167,168,169,170,171,173,174,175,177,178,179,180,181,183,184,185,186,187,189,190,191,193,194,195,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,219,221,222,223,225,226,227,228,229,231,233,234,235,237,238,239,241,243,245,247,249],
+  "name": "pas"
+ }],
+ "parent_index": [0,0,1,0,3,0,5,0,7,0,9,0,11,12,13,14,15,0,17,2,19,4,21,4,23,6,25,26,27,28,29,6,31,32,33,34,35,8,37,8,39,40,41,10,43,10,45,46,47,48,49,50,51,18,53,18,55,20,57,22,59,22,61,24,63,64,65,66,67,24,69,70,71,30,73,30,75,36,77,36,79,38,81,38,83,84,85,42,87,42,89,44,91,92,93,94,95,44,97,98,99,100,101,52,103,52,105,54,107,108,109,110,111,54,113,114,115,116,117,56,119,120,121,122,123,56,125,126,127,128,129,60,131,60,133,134,135,62,137,138,139,140,141,142,143,62,145,82,147,148,149,150,151,82,153,154,155,90,157,90,159,160,161,132,163,164,165,166,167,168,169,170,171,132,173,174,175,136,177,178,179,180,181,136,183,184,185,186,187,146,189,190,191,146,193,194,195,172,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,172,217,218,219,176,221,222,223,176,225,226,227,228,229,216,231,216,233,234,235,220,237,238,239,220,241,232,243,232,245,236,247,236,249]
+}]
diff --git a/main.cpp b/main.cpp
index e15fb88707d58ee6b0b72670e7559bcf0d5eb360..9ad116b0d8a2d06624e64f3c5683190e4d942dbe 100644
--- a/main.cpp
+++ b/main.cpp
@@ -221,24 +221,23 @@ TEST(cell_tree, balance) {
     }
 }
 
-/*
 void test_json() {
     json  cell_data;
     std::ifstream("cells_small.json") >> cell_data;
 
-    for(auto c : range(0,20)) {
-    //for(auto c : range(0,cell_data.size())) {
+    for(auto c : range(0,cell_data.size())) {
         std::vector<int> parent_index = cell_data[c]["parent_index"];
         cell_tree tree(parent_index);
         std::cout << "cell " << c << " ";
-        tree.balance();
-        tree.to_graphviz("cell_" + std::to_string(c) + ".dot");
-        std::cout << memory::util::yellow("---------") << std::endl;
+        //tree.balance();
+        //tree.to_graphviz("cell_" + std::to_string(c) + ".dot");
+        tree.to_graphviz("cell" + std::to_string(c) + ".dot");
+        //std::cout << memory::util::yellow("---------") << std::endl;
     }
 }
-*/
 
 int main(int argc, char **argv) {
+    test_json();
     ::testing::InitGoogleTest(&argc, argv);
     return RUN_ALL_TESTS();
 }
diff --git a/make_image.sh b/make_image.sh
index d4e6c1031196c73c2a441ebd3644e8629691cab8..c3b4a91096bba267810067fceebfe73c8ee271d8 100755
--- a/make_image.sh
+++ b/make_image.sh
@@ -1,2 +1,5 @@
 dot cell.dot -Tpdf -o cell.pdf
-open cell.pdf
+# uses display from imagemagik
+display cell.pdf
+# or just call open on os x
+#open cell.pdf
diff --git a/makefile b/makefile
index 4faf5d8f467f666c7aba7527eabdd48d016c153c..3a75e5b6907eb4c1efd25d95d5ed8e521d911831 100644
--- a/makefile
+++ b/makefile
@@ -2,7 +2,7 @@ CC=clang++
 FLAGS=-std=c++11 -g
 
 test.exe : main.cpp *.hpp makefile gtest.o
-	$(CC) $(FLAGS) main.cpp -o test.exe gtest.o
+	$(CC) $(FLAGS) main.cpp -o test.exe gtest.o -pthread
 
 gtest.o :
 	$(CC) $(FLAGS) gtest-all.cc -c -o gtest.o
diff --git a/tree.hpp b/tree.hpp
index 6edc61e77ae2d12b60d77b0d61ac2499fdd40f1d..3645042ebf3346d9df0f74911bd4217664e96a9d 100644
--- a/tree.hpp
+++ b/tree.hpp
@@ -187,11 +187,6 @@ class tree {
         tree new_tree;
         new_tree.init(num_nodes());
 
-        // mark all nodes
-        new_tree.parents_(memory::all) = -1;
-        new_tree.child_index_(memory::all) = -1;
-        new_tree.children_(memory::all) = -1;
-
         // add the root node
         new_tree.parents_[0] = -1;
         new_tree.child_index_[0] = 0;
@@ -210,6 +205,8 @@ class tree {
             new_tree.children_.begin(), [&p] (int i) {return p[i];}
         );
 
+        //std::swap(data_, new_tree.data_);
+
         return new_tree;
     }
 
@@ -313,6 +310,7 @@ class tree {
     }
 
     index_type data_;
+
     index_view children_;
     index_view child_index_;
     index_view parents_;