Dendritica (Vetter et al 2001)

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Accession:7907
Dendritica is a collection of programs for relating dendritic geometry and signal propagation. The programs are based on those used for the simulations described in: Vetter, P., Roth, A. & Hausser, M. (2001) For reprint requests and additional information please contact Dr. M. Hausser, email address: m.hausser@ucl.ac.uk
Reference:
1 . Vetter P, Roth A, Häusser M (2001) Propagation of action potentials in dendrites depends on dendritic morphology. J Neurophysiol 85:926-37 [PubMed]
Citations  Citation Browser
Model Information (Click on a link to find other models with that property)
Model Type: Dendrite;
Brain Region(s)/Organism:
Cell Type(s): Hippocampus CA1 pyramidal GLU cell; Hippocampus CA3 pyramidal GLU cell; Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; Cerebellum Purkinje GABA cell;
Channel(s): I Na,t; I L high threshold; I p,q; I K; I M; I K,Ca;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Action Potential Initiation; Bursting; Active Dendrites; Influence of Dendritic Geometry; Detailed Neuronal Models; Axonal Action Potentials; Action Potentials;
Implementer(s): Hausser, M [M.Hausser at ucl.ac.uk];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal GLU cell; Hippocampus CA3 pyramidal GLU cell; Cerebellum Purkinje GABA cell; Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; I Na,t; I L high threshold; I p,q; I K; I M; I K,Ca;
Files displayed below are from the implementation
/* converted by pv 30/9/98

 Data published in:

 Rihn, L. and  Claiborne, B.J.  Dendritic growth and regression 
in rat dentate granule cells during late postnatal development.  
Dev. Brain Research 54 (1990) 115-124.

Dentate Granule Cell:

Labeling Method: Intracellular injection using HRP filled 
                 sharp electrodes in thick 400um thick
                 whole-mounts.

Cell id: 411884b.out 

Animal:  Sprague Dawley Rat  obtained from Harlan Sprague Dawley

Age of animal:  Postnatal day   38

*Location:  Suprapyramidal blade of the dentate gyrus

   		-- Layer position of cell     2.3    

                     (0 bottom - 6 top of cell body layer)
		
                -- Blade Position of cell     3.5    
                     
                     (0 near crest - 6 tip of suprapyramidal blade)

* A gradient referring to the location of the cell.   
	dummy = fscan()


 */


seg= 230
sommax = 4 
                                                /* variable arrayvals */
double comp[seg],pare[seg],xval[seg],yval[seg],zval[seg],len[seg],dia[seg]
double peakit[seg]
create dend[seg]                                /* creates the comparetments */
create soma

proc geometry() { 
 
for i=0,seg-1 {                                 /* read in variables */
		comp[i] = fscan()
	        pare[i] = fscan()
		dummy = fscan()
	        xval[i] = fscan()
        	yval[i] = fscan()
	        zval[i] = fscan()
        	dia[i] = fscan() 
	        len[i] = fscan()
		dummy_termination = fscan()
		}
 
  
soma { 	for i = 0,sommax {   pt3dadd(xval[i],yval[i],zval[i],dia[i]) }
	nseg = int(L/5)
     }	


 for i=sommax+1,seg-1 {                                 /* all other comparetments */
         	dend[i] {
			nseg=1 
			pt3dadd(xval[pare[i]],yval[pare[i]],zval[pare[i]],dia[pare[i]])
			pt3dadd(xval[i],yval[i],zval[i],dia[i]) 	
			}
 		}
  
 for i=1,seg-1 {  if (pare[i] > sommax) dend[pare[i]] connect dend[i](0),1 else {

					 soma	       connect dend[i](0),pare[i]/sommax } 
		}

for i = 0,sommax { dend[i] delete_section() }

}

geometry()

SOMA

0	-1	1	0.2	-0.2	0	4.51	0.01	0
1	0	2	0.99	4.31	0	8.11	4.57867	0
2	1	3	2.32	8.59	0	9.91	4.48189	0
3	2	4	3.38	14.44	-3.44	4.96	6.86875	0
4	3	10	2.01	20.4	-2.7	3.6	6.16004	0


DENDRITIC TREE

5	4	11	1.74	24.68	-2.7	3.6	4.28851	0
6	5	12	2.01	27.61	-2.7	3.15	2.94241	-1
7	6	18	2.01	34.59	-2.7	3.15	6.98	0
8	7	17	1.74	33.69	-2.7	3.15	0.939628	0
9	8	19	2.01	35.04	-2.29	2.25	1.43649	0
10	9	20	1.74	36.17	-3.93	2.25	2.00983	-1
11	10	21	3.33	40.23	-0.15	2.7	5.77062	0
12	11	22	2.54	51.69	4.42	2.7	12.3629	0
13	12	23	2.81	56.87	8.18	2.7	6.40647	0
14	13	24	3.07	62.5	8.18	2.7	5.636	0
15	14	25	3.53	71.16	13.38	2.7	10.1117	0
16	15	26	3.53	77.02	12.77	2.7	5.89166	0
17	16	29	3.47	75.47	18.5	2.25	5.93624	-1
18	17	31	3.47	82.67	13.34	2.25	8.85808	0
19	18	32	3.74	87.4	13.34	2.25	4.7377	0
20	19	33	4.26	91.68	13.34	2.25	4.31147	0
21	20	34	4.26	94.61	13.34	2.25	2.93	-1
22	21	35	6.91	101.15	13.34	2.25	7.05649	0
23	22	36	8.5	110.83	13.34	2.25	9.80971	0
24	23	37	10.19	118.91	13.34	2.25	8.25485	0
25	24	38	12.84	128.37	17.14	2.25	10.5335	0
26	25	39	15.45	135.06	18.06	2.25	7.23979	0
27	26	40	18.1	144.52	15.78	2.25	10.0853	0
28	27	41	19.95	153.08	15.78	2.25	8.75763	0
29	28	42	22.05	166.07	15.78	2.25	13.1587	0
30	29	43	24.17	175.3	15.78	2.25	9.47034	0
31	30	44	25.79	182.13	15.78	2.25	7.01949	0
32	31	45	26.05	184.16	15.78	2.25	2.04658	-1
33	32	46	31.88	190.47	15.78	2.25	8.59098	0
34	33	47	36.12	197.45	15.78	2.25	8.16688	0
35	34	48	41.23	206.41	15.34	2.25	10.3241	0
36	35	49	45.2	211.14	15.34	2.25	6.17526	0
37	36	50	51.29	219.93	13.46	2.25	10.8576	0
38	37	51	55.64	226.78	10.92	2.25	8.50274	0
39	38	52	57.75	229.71	10.92	1.8	3.61068	0
40	39	53	59.61	232.42	10.92	1.8	3.2869	0
41	40	54	60.93	236.92	10.92	1.8	4.68961	0
42	41	55	63.05	238.5	9.22	1.8	3.14337	0
43	42	56	68.76	241.35	9.22	1.8	6.38174	0
44	43	57	72.2	245.41	12.79	1.8	6.40797	0
45	44	58	75.65	250.59	12.79	1.8	6.22374	0
46	45	59	78.82	254.19	12.79	1.8	4.79676	0
47	46	60	81.21	258.25	12.79	1.8	4.71123	0
48	47	61	84.31	264.31	12.79	1.8	6.80688	0
49	48	62	86.43	268.14	12.79	1.8	4.37759	0
50	49	63	88.28	271.29	12.79	1.8	3.65308	0
51	50	64	89.61	273.77	12.79	1.8	2.81413	0
52	51	65	91.73	278.5	12.79	1.8	5.18337	0
53	52	66	93.85	280.23	16.52	1.8	4.62604	-2
54	32	67	28.05	194.59	19.22	1.8	11.1633	0
55	54	68	29.11	203.82	15.48	1.8	10.0152	0
56	55	69	28.41	207.83	15.48	1.8	4.07064	0
57	56	70	29.99	215.26	15.48	1.8	7.59614	0
58	57	71	31.58	221.8	16.78	1.8	6.8549	0
59	58	72	31.58	231.48	16.33	1.8	9.69045	0
60	59	73	32.33	231.63	16.93	1.8	0.972111	-1
61	60	74	33.65	236.81	21.41	1.8	6.97461	0
62	61	75	33.65	242.21	21.41	1.8	5.4	0
63	62	76	33.92	250.55	24.38	1.8	8.85717	0
64	63	77	35.59	260.34	24.38	1.8	9.93141	0
65	64	78	36.91	266.19	24.38	1.8	5.99707	0
66	65	79	38.24	274.75	24.38	1.8	8.66271	0
67	66	80	39.26	280.18	26.58	1.8	5.94687	0
68	67	81	43.76	286.04	28.9	1.8	7.74416	0
69	68	82	44.29	292.57	28.3	1.8	6.57889	0
70	69	83	44.55	298.43	33.45	1.8	7.80575	0
71	70	84	41.95	302.93	33.44	1.8	5.19712	-2
72	60	85	31.81	239.06	16.08	1.8	7.49652	0
73	72	86	31.81	245.14	16.08	1.8	6.08	0
74	73	87	32.34	248.52	16.08	1.8	3.4213	0
75	74	88	33.66	255.05	16.08	1.8	6.66208	0
76	75	89	35.06	261.06	16.08	1.8	6.17091	0
77	76	90	35.06	271.64	16.08	1.8	10.58	0
78	77	91	35.85	279.3	17.57	1.8	7.84346	0
79	78	92	35.01	289.34	17.57	1.8	10.0751	0
80	79	93	34.48	296.55	17.57	1.8	7.22945	0
81	80	94	35.01	306.91	17.57	1.8	10.3735	0
82	81	95	36.79	318.26	17.57	1.8	11.4887	0
83	82	96	37.05	321.64	18.86	1.8	3.62713	-2
84	21	97	2.61	104.64	13.34	2.25	10.1648	0
85	84	98	3.14	108.92	13.34	2.25	4.31269	0
86	85	99	-0.3	119.73	16.22	1.8	11.704	0
87	86	100	-2.65	122.58	16.22	1.8	3.69391	0
88	87	101	-5.57	136.79	13.78	1.8	14.7107	0
89	88	102	-6.89	147.16	12.67	1.8	10.5124	0
90	89	103	-7	151.73	13.75	1.8	4.69717	0
91	90	104	-8.85	161.19	13.75	1.8	9.6392	0
92	91	105	-10.44	171.1	12.3	1.8	10.1409	0
93	92	106	-11.99	179.56	15.72	1.8	9.25584	0
94	93	107	-11.99	190.15	15.72	1.8	10.59	0
95	94	108	-15.24	200.39	16.36	1.8	10.7624	0
96	95	109	-17.89	208.95	17.06	1.8	8.98811	0
97	96	110	-19.39	218.49	19.81	1.8	10.0411	0
98	97	111	-22.57	230.43	19.34	1.8	12.3651	0
99	98	112	-24.78	238.74	22.36	1.8	9.11376	0
100	99	113	-26.9	247.3	22.36	1.8	8.81862	0
101	100	114	-28.75	252.48	22.36	1.8	5.50045	0
102	101	115	-30.06	253.75	22.36	1.8	1.82455	-1
103	102	116	-29.79	263.44	21.98	1.8	9.70121	0
104	103	117	-30.59	271.1	24.26	1.8	8.03206	0
105	104	118	-28.81	275.51	23.27	1.8	4.85763	0
106	105	119	-30.4	285.42	23.27	1.8	10.0367	0
107	106	120	-31.46	293.98	24.81	1.8	8.76178	0
108	107	121	-32.72	298.23	24.81	1.8	4.43284	0
109	108	122	-32.99	303.86	27.06	1.8	6.06896	0
110	109	123	-32.46	307.02	26.88	1.8	3.20919	0
111	110	124	-30.08	309.49	31.21	1.8	5.52397	0
112	111	125	-27.16	309.94	29.14	1.8	3.60746	-2
113	102	126	-36.08	266.09	26.21	1.8	14.2597	0
114	113	127	-39.26	272.85	26.21	1.8	7.47061	0
115	114	128	-46.94	280.23	26.21	1.8	10.6511	0
116	115	129	-50.65	285.19	26.28	1.8	6.1944	0
117	116	130	-53.03	289.47	29.3	1.8	5.75354	0
118	117	131	-56.21	293.52	29.3	1.8	5.14926	0
119	118	132	-59.38	300.78	32.38	1.8	8.49958	0
120	119	133	-63.61	307.09	33.1	1.8	7.63069	0
121	120	134	-66.79	312.05	37.56	1.8	7.38956	0
122	121	135	-70.84	314.25	37.56	1.8	4.60896	0
123	122	136	-73.22	315.38	34.24	1.8	4.23836	-2
124	17	137	4.39	80.71	17.97	1.8	5.34648	0
125	124	138	4.92	86.11	17.97	1.8	5.42595	0
126	125	139	5.19	92.42	21.45	2.25	7.21106	0
127	126	140	5.72	100.31	23.42	2.25	8.14947	0
128	127	141	5.21	106.51	24.74	2.25	6.35944	0
129	128	142	4.94	109.66	24.74	2.25	3.16155	0
130	129	143	5.21	112.36	27.91	2.25	4.17274	-1
131	130	144	7.85	116.42	27.91	1.8	4.84285	0
132	131	145	10.77	120.7	27.91	1.8	5.1812	0
133	132	146	14.51	125.33	26.76	1.8	6.06193	0
134	133	147	17.95	129.61	26.76	1.8	5.49108	0
135	134	148	22.72	135.24	29.42	1.8	7.84381	0
136	135	149	25.89	139.97	29.42	1.8	5.69401	0
137	136	150	28.98	142.28	29.42	1.8	3.858	0
138	137	151	31.1	147.46	33.66	1.8	7.02171	0
139	138	152	34.27	152.87	33.66	1.8	6.27033	0
140	139	153	37.98	159.85	38.18	1.8	9.10576	0
141	140	154	41.11	165.71	38.18	1.8	6.64353	0
142	141	155	42.97	171.56	37.9	1.8	6.14496	0
143	142	156	45.35	178.32	39.88	1.8	7.43521	0
144	143	157	48.31	183.16	45.9	1.8	8.2721	0
145	144	158	52.02	188.79	45.9	1.8	6.74248	0
146	145	159	53.87	192.84	46.74	1.8	4.53107	0
147	146	160	56.52	199.15	51.47	1.8	8.31934	0
148	147	161	59.18	204.86	50.61	1.8	6.35762	0
149	148	162	62.89	210.26	52.73	1.8	6.88611	0
150	149	163	65.8	215.22	54.84	1.8	6.1255	0
151	150	164	67.66	222.43	59.94	1.8	9.02517	0
152	151	165	73.69	227.78	59.94	1.8	8.06123	0
153	152	166	76.87	235.89	59.88	1.8	8.71138	0
154	153	167	80.57	242.42	63.91	1.8	8.51891	0
155	154	168	84.24	246.23	63.91	1.8	5.29009	0
156	155	169	87.15	254.11	66.46	1.8	8.77867	0
157	156	170	89.27	256.82	66.46	1.8	3.44071	0
158	157	171	92.98	263.12	67.22	1.8	7.35063	0
159	158	172	95.05	265.23	68.93	1.8	3.41484	0
160	159	173	98.23	266.8	68.93	1.8	3.54645	0
161	160	174	99.29	270.63	68.93	1.8	3.97398	0
162	161	175	104.59	279.42	70.46	1.8	10.3776	0
163	162	176	107.5	284.6	71.31	1.8	6.00192	0
164	163	177	105.81	292.23	71.31	1.8	7.81492	0
165	164	178	110.58	303.5	70.44	1.8	12.2688	0
166	165	179	113.71	307.23	69.54	1.8	4.95175	0
167	166	180	115.57	309.03	68.57	1.8	2.76415	-2
168	130	181	3.74	117.38	26.7	1.8	5.36893	0
169	168	182	5.06	116.48	43.92	1.8	17.294	-1
170	169	183	7.45	119.63	43.92	1.8	3.95406	0
171	170	184	6.92	131.12	49.83	1.8	12.9317	0
172	171	185	5.35	135.08	56.1	1.8	7.5802	0
173	172	186	6.67	144.09	63.94	1.8	12.0162	0
174	173	187	7.2	149.72	64.36	1.8	5.67047	0
175	174	188	3.69	162.02	68.15	1.8	13.3407	0
176	175	189	1.31	167.42	72.73	1.8	7.46999	0
177	176	190	-2.13	172.15	73.82	1.8	5.94934	0
178	177	191	-2.4	180.74	82.24	1.8	12.0315	0
179	178	192	-2.93	184.79	87.27	1.8	6.47953	-2
180	169	193	4.21	124.89	26.72	1.8	19.1648	0
181	180	194	4.21	125.34	29.16	1.8	2.48115	-1
182	181	195	4.21	130.07	30.82	1.8	5.01283	0
183	182	196	4.74	138.63	34.5	1.8	9.33257	0
184	183	197	4.47	147.16	36.79	1.8	8.83617	0
185	184	198	4.21	153.69	39.59	1.8	7.10975	0
186	185	199	4.47	159.55	42.42	1.8	6.51276	0
187	186	200	3.54	167.26	42.42	1.8	7.76589	0
188	187	201	3.54	171.54	43.33	1.8	4.37567	0
189	188	202	1.95	174.47	47.6	1.8	5.41719	0
190	189	203	1.95	183.7	48.58	1.8	9.28188	0
191	190	204	0.41	188.96	50.61	1.8	5.84466	0
192	191	205	-0.65	198.87	52.4	1.8	10.126	0
193	192	206	-0.65	206.08	60.45	1.8	10.8068	0
194	193	207	0.13	212.76	65.15	1.8	8.20493	0
195	194	208	0.92	217.94	67.98	1.8	5.95528	0
196	195	209	1.19	222.9	71.71	1.8	6.21188	0
197	196	210	0.13	227.4	74.2	1.8	5.25107	0
198	197	211	-0.39	234.41	81.09	1.8	9.8429	0
199	198	212	0.93	240.49	79.82	1.8	6.34994	0
200	199	213	0.66	241.62	78.53	1.8	1.73606	-2
201	181	214	2.61	134.69	29.16	1.8	9.48591	0
202	201	215	0.23	144.15	27.13	1.8	9.96378	0
203	202	216	-1.72	152.76	27.13	1.8	8.82806	0
204	203	217	-3.78	162.21	27.13	1.8	9.67192	0
205	204	218	-5.9	170.55	27.87	1.8	8.63699	0
206	205	219	-6.17	182.94	28.77	1.8	12.4256	0
207	206	220	-8.91	189.31	28.77	1.8	6.9343	0
208	207	221	-11.03	199.22	27.19	1.8	10.2567	0
209	208	222	-14.47	210.03	26.58	1.8	11.3605	0
210	209	223	-16.78	221.06	28.58	1.8	11.4454	0
211	210	224	-17.05	233	32.49	1.8	12.5668	0
212	211	225	-21.04	243.34	34.26	1.8	11.2236	0
213	212	226	-22.36	249.64	37.48	1.8	7.19728	0
214	213	227	-26.07	260.91	36.29	1.8	11.9245	0
215	214	228	-26.73	270.04	36.29	1.8	9.15382	0
216	215	229	-30.44	282.2	37.95	1.8	12.8213	0
217	216	230	-34.97	297.52	40.34	1.8	16.1535	0
218	217	231	-39.73	311.26	40.34	1.8	14.5412	0
219	218	232	-42.25	315.25	40.34	1.8	4.71916	0
220	219	233	-40.92	318.86	42.42	1.8	4.37349	-2
221	10	234	1.8	47.82	-11.08	2.25	13.6693	0
222	221	235	-0.05	58.85	-9.85	2.25	11.2515	0
223	222	236	-1.12	62.85	-9.85	2.25	4.14064	0
224	223	237	-0.86	67.36	-9	1.8	4.59676	0
225	224	238	-4.04	71.19	-6.41	1.8	5.61154	0
226	225	239	-5.89	76.6	-9.77	2.25	6.63176	0
227	226	240	-7.21	89.21	-9.53	2.25	12.6812	0
228	227	241	-9.25	98.04	-9.53	2.25	9.06259	-2
229	6	16	1.74	29.41	-2.7	3.15	1.82014	-2