Neuron recipes

The diffusion MRI signal arising from neurons can be numerically simulated by solving the Bloch-Torrey partial differential equation. In order to facilitate the diffusion MRI simulation of realistic neurons by the research community, we constructed finite element meshes for a group of 36 pyramidal neurons and a group of 29 spindle neurons whose morphological descriptions were found in the publicly available neuron repository NeuroMopho.org. These finite elements meshes range from having 15163 nodes to 622553 nodes. We also broke the neurons into the soma and dendrite branches and created finite elements meshes for these cell components. Through the Neuron Module, these neuron and components finite element meshes can be seamlessly coupled with the functionalities of SpinDoctor to provide the diffusion MRI signal that can be attributed to spins inside neurons.

The neuron mesh files are available at https://github.com/SpinDoctorMRI/RealNeuronMeshes.

The table below lists the names and the finite element mesh sizes of the group of 36 pyramidal neurons and the group of 29 spindle neurons.

Neuron ID	Num. of FE mesh nodes	Neuron ID	Num. of FE mesh nodes
03a_spindle2aFI	38202	02a_pyramidal2aFI	119156
03a_spindle6aFI	44000	02b_pyramidal1aACC	45216
03b_spindle4aACC	17370	02b_pyramidal1aFI	105384
03b_spindle5aACC	26345	03a_pyramidal9aFI	81530
03b_spindle6aACC	26792	03b_pyramidal2aACC	28183
03b_spindle7aACC	21618	03b_pyramidal3aACC	27607
04b_spindle3aFI	51265	03b_pyramidal3aFI	151362
05b_spindle5aFI	22457	03b_pyramidal4aFI	96177
06b_spindle8aACC	15163	03b_pyramidal9aFI	66162
07b_spindle9aACC	54952	04a_pyramidal4aACC	150897
08a_spindle13aACC	46293	04a_pyramidal5aACC	89256
09o_spindle7aFI	38992	04b_pyramidal5aFI	95784
09o_spindle8aFI	60755	04b_pyramidal6aACC	87195
10a_spindle18aACC	25797	04b_pyramidal6aFI	90482
12a_spindle19aACC	31841	04b_pyramidal7aACC	622553
12o_spindle9aFI	29320	05a_pyramidal10aACC	201506
13o_spindle10aFI	43081	05a_pyramidal8aACC	139975
15o_spindle12aFI	101548	05b_pyramidal7aFI	208203
16o_spindle13aFI	18266	05b_pyramidal8aFI	124350
19o_spindle14aFI	25786	05b_pyramidal9aACC	366659
21o_spindle15aFI	28822	06a_pyramidal11aACC	319574
23o_spindle16aFI	30073	06b_pyramidal10aFI	106808
25o_spindle17aFI	52919	06b_pyramidal12aACC	277718
26o_spindle18aFI	36239	07a_pyramidal13aACC	155854
27o_spindle19aFI	50807	07b_pyramidal14aACC	309789
28o_spindle20aFI	56036	08o_pyramidal11aFI	419651
28o_spindle21aFI	17581	10a_pyramidal15aACC	56184
29o_spindle22aFI	18414	11a_pyramidal16aACC	222732
30o_spindle23aFI	26357	11o_pyramidal12aFI	380293
22o_pyramidal16aFI	389878	17o_pyramidal13aFI	326989
24o_pyramidal17aFI	245058	18o_pyramidal14aFI	338453
25o_pyramidal18aFI	71209	20o_pyramidal15aFI	247116
31o_pyramidal19aFI	619390

The following table shows the morphological characteristics for the neurons.

Neuron ID	Brain region	Avg. dia. $(\mu m)$	Height $(\mu m)$	Soma vol. $(\mu m^3)$	Total vol. $(\mu m^3)$
02a_pyramidal2aFI	fronto-insula	1.27	404.85	19701.05	25639.61
02b_pyramidal1aACC	anterior cingulate	1.58	363.08	9065.56	11579.71
02b_pyramidal1aFI	fronto-insula	1.62	381.56	22475.52	29804.96
03a_pyramidal9aFI	fronto-insula	2.15	532.30	22557.27	30189.28
03a_spindle2aFI	fronto-insula	1.74	387.16	13406.27	17684.23
03a_spindle6aFI	fronto-insula	1.66	501.47	33458.19	37812.72
03b_pyramidal2aACC	anterior cingulate	1.48	189.29	2977.21	4487.44
03b_pyramidal3aACC	anterior cingulate	1.14	188.45	6005.06	6891.04
03b_pyramidal3aFI	fronto-insula	1.84	496.35	32510.62	46154.08
03b_pyramidal4aFI	fronto-insula	1.33	414.70	35253.85	39324.87
03b_pyramidal9aFI	fronto-insula	1.92	430.06	15263.14	20532.57
03b_spindle4aACC	anterior cingulate	1.43	336.33	3098.39	4070.19
03b_spindle5aACC	anterior cingulate	1.49	221.52	11925.78	13242.53
03b_spindle6aACC	anterior cingulate	1.33	398.36	4027.74	6058.67
03b_spindle7aACC	anterior cingulate	1.18	369.51	4982.41	6076.52
04a_pyramidal4aACC	anterior cingulate	1.52	705.96	5684.55	13637.33
04a_pyramidal5aACC	anterior cingulate	1.86	410.59	15010.43	24648.35
04b_pyramidal5aFI	fronto-insula	1.78	480.13	10312.87	17184.26
04b_pyramidal6aACC	anterior cingulate	1.41	465.88	3129.97	7497.12
04b_pyramidal6aFI	fronto-insula	1.56	310.21	14718.05	21708.21
04b_pyramidal7aACC	anterior cingulate	1.3	610.42	17060.60	28552.49
04b_spindle3aFI	fronto-insula	2.71	391.14	22569.99	28404.13
05a_pyramidal10aACC	anterior cingulate	1.74	281.20	16604.06	21826.41
05a_pyramidal8aACC	anterior cingulate	1.29	430.37	24709.77	29778.79
05b_pyramidal7aFI	fronto-insula	2.18	281.02	25720.11	32731.05
05b_pyramidal8aFI	fronto-insula	1.66	361.45	32527.06	44679.46
05b_pyramidal9aACC	anterior cingulate	1.56	650.60	23948.05	40014.54
05b_spindle5aFI	fronto-insula	2.35	381.88	15383.08	18190.63
06a_pyramidal11aACC	anterior cingulate	1.46	437.60	17222.02	29995.02
06b_pyramidal10aFI	fronto-insula	1.92	365.18	43127.81	52179.53
06b_pyramidal12aACC	anterior cingulate	1.52	324.94	17181.33	24931.32
06b_spindle8aACC	anterior cingulate	1.92	342.21	18237.49	19462.92
07a_pyramidal13aACC	anterior cingulate	1.37	325.73	6254.53	8738.01
07b_pyramidal14aACC	anterior cingulate	1.67	350.40	16053.07	22772.96
07b_spindle9aACC	anterior cingulate	1.75	437.87	21344.83	27307.48
08a_spindle13aACC	anterior cingulate	1.74	814.45	9911.07	14113.32
08o_pyramidal11aFI	fronto-insula	1.91	421.68	11512.38	24326.94
09o_spindle7aFI	fronto-insula	2.90	472.87	22052.10	27905.89
09o_spindle8aFI	fronto-insula	2.05	376.73	11923.76	15189.32
10a_pyramidal15aACC	anterior cingulate	1.40	341.48	8522.11	10960.84
10a_spindle18aACC	anterior cingulate	1.57	457.90	5895.17	7219.28
11a_pyramidal16aACC	anterior cingulate	1.27	486.31	8807.01	12263.84
11o_pyramidal12aFI	fronto-insula	1.91	369.34	70786.62	79516.92
12a_spindle19aACC	anterior cingulate	2.05	431.22	12178.08	15618.67
12o_spindle9aFI	fronto-insula	3.41	305.31	29983.79	36678.18
13o_spindle10aFI	fronto-insula	2.69	516.92	39866.55	46022.15
15o_spindle12aFI	fronto-insula	3.60	604.57	53192.65	79170.43
16o_spindle13aFI	fronto-insula	2.17	364.66	17467.88	18888.13
17o_pyramidal13aFI	fronto-insula	1.89	340.77	11004.30	21167.19
18o_pyramidal14aFI	fronto-insula	1.74	288.41	69851.56	78999.20
19o_spindle14aFI	fronto-insula	2.18	232.21	10507.15	12905.43
20o_pyramidal15aFI	fronto-insula	1.82	383.18	22344.32	27667.19
21o_spindle15aFI	fronto-insula	2.36	286.33	17567.69	29466.53
22o_pyramidal16aFI	fronto-insula	1.94	585.35	18776.05	29441.43
23o_spindle16aFI	fronto-insula	1.67	420.05	10429.13	13482.93
24o_pyramidal17aFI	fronto-insula	2.04	371.99	40986.40	47377.09
25o_pyramidal18aFI	fronto-insula	1.80	364.05	18587.13	23572.15
25o_spindle17aFI	fronto-insula	1.79	358.70	7897.44	13563.26
26o_spindle18aFI	fronto-insula	2.27	442.65	52911.93	56084.44
27o_spindle19aFI	fronto-insula	1.73	275.08	20640.14	25423.96
28o_spindle20aFI	fronto-insula	3.00	520.69	35442.59	51267.07
28o_spindle21aFI	fronto-insula	2.62	298.57	35579.06	37783.31
29o_spindle22aFI	fronto-insula	3.52	402.84	62928.22	83279.12
31o_pyramidal19aFI	fronto-insula	2.26	303.55	65950.80	86376.72

The neuron models and the measurement data are from (Ascoli 2007) and (Watson 2006).