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234 lines
11 KiB
234 lines
11 KiB
# -*- encoding: utf-8 -*- |
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from ._db import add_table_data |
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#: Mouse synaptic convregence table |
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mouse_convergence = u""" |
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|
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Convergence defines the average number of presynaptic cells of a particular |
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type (rows) that synapse onto a single postsynaptic cell of a particular |
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type (columns). |
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This connectivity matrix is currently incomplete. |
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Note: Bushy and pyramidal cells are known to have no (or very few) |
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collaterals within the CN, and so they are not listed as presynaptic cells in |
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this table. Octopus cells have collaterals (including in granule cell domains), |
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and should be added to this table when more data are available (Golding et al., |
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J. Neurosci. 15: 3138, 1995) |
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---------------------------------------------------------------------------------------------- |
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bushy tstellate dstellate octopus pyramidal tuberculoventral |
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sgc 3.3±0.6 [2] 6.5±1.0 [2] 35±0 [3] 60±0 [2] 48±0 [5] 24±0 [5] |
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dstellate 7 [1] 20 [1] 3 [1] 0 [4] 15 [5] 15 [5] |
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tstellate 0 [6] 0 [6] 0 [6] 0 [6] 0 [6] 0 [6] |
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tuberculoventral 6 6 0 0 [4] 21 [5] 0 [7] |
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pyramidal 0 0 0 0 0 0 |
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---------------------------------------------------------------------------------------------- |
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[1] Guesses based on Campagnola & Manis 2014 |
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|
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[2] Cao, X. & Oertel, D. (2010). Auditory nerve fibers excite targets through |
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synapses that vary in convergence, strength, and short-term plasticity. |
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Journal of Neurophysiology, 104(5), 2308–20. |
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Xie and Manis (unpublished): max EPSC = 3.4 ± 1.5 nA with ~0.3 nA steps |
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(Cao and Oertel, 2010) = ~11 AN inputs. However neither we nor Cao and Oertel |
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see that many clear steps in the responses, so use lower bound. |
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|
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[3] Lower bound based on estimates from unpublished data Xie and Manis (2017) |
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Assumptions: No discernable step sizes when increasing shock intensity |
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at ANFs in radiate multipolars (dstellate) |
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Measured: 0.034 ± 15 nA sEPSC @ -70 mV |
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Measured: Maximal current from AN stim = 1.2 ± 0.7 nA @ -70 mV |
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Assuming that each AN provides 1 input, then N = ~35 |
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|
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[4] Octopus cells are devoid of inhibitory input (Golding et al., J. Neurosci., 1995) |
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|
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[5] Convergence from Hancock and Voigt, Ann. Biomed. Eng. 27, 1999 and Zheng and Voigt, |
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Ann. Biomed. Eng., 34, 2006. Numbers are based on models for cat and gerbil, |
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respectively. Adjusted to 1/2 to avoid overexciting TV cells in network model. |
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|
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[6] tstellate cells have collaterals within the CN. It has been proposed that they |
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provide auditory-driven input to the DCN (Oertel and Young, ), and also synapse |
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within the VCN (Oertel, SFN abstract). These parameters may need to be adjusted |
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once the convergence and strength is known. |
|
|
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[7] In the models of Hancock and Voigt (1999) and Zheng and Voigt (2006), the TV cells |
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have no connections with each other. However, Kuo et al. (J. Neurophysiol., 2015) |
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did see connections between pairs of TV cells in the mouse. |
|
|
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""" |
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add_table_data( |
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"convergence", |
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row_key="pre_type", |
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col_key="post_type", |
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species="mouse", |
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data=mouse_convergence, |
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) |
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mouse_convergence_range = u""" |
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|
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The convergence range table describes, for each type of connection from |
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presynaptic (rows) to postsynaptic (columns), the variance in frequency of |
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presynaptic cells relative to the postsynaptic cell. |
|
|
|
All values are expressed as the sigma for a lognormal distribution scaled to |
|
the CF of the postsynaptic cell. |
|
|
|
---------------------------------------------------------------------------------------------- |
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bushy tstellate dstellate octopus pyramidal tuberculoventral |
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sgc 0.05 [1] 0.1 [1] 0.4 [1] 0.5 [5] 0.1 [1] 0.1 [1] |
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dstellate 0.208 [2] 0.347 [2] 0.5 [1] 0 0.2 [1] 0.2 [1] |
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tstellate 0.1 [4] 0.1 [4] 0 0 0 0 |
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tuberculoventral 0.069 [3] 0.111 [3] 0 0 0.15 [1] 0 |
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pyramidal 0 0 0 0 0 0 |
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---------------------------------------------------------------------------------------------- |
|
|
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[1] Guess based on axonal / dendritic morphology. |
|
|
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[2] Calculated from Campagnola & Manis 2014 fig. 7C |
|
Distribution widths are given in stdev(octaves), so we multiply by ln(2) to |
|
get the sigma for a lognormal distribution. |
|
DS->Bushy: ln(2) * 0.3 = 0.208 |
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DS->TStellate: ln(2) * 0.5 = 0.347 |
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|
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[3] Calculated from Campagnola & Manis 2014 fig. 9C |
|
Distribution widths are given in stdev(octaves), so we multiply by ln(2) to |
|
get the sigma for a lognormal distribution. |
|
TV->Bushy: ln(2) * 0.10 = 0.069 |
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TV->TStellate: ln(2) * 0.16 = 0.111 |
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|
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[4] Guess based on very limited information in Campagnola & Manis 2014 fig. 12 |
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|
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[5] Octopus cells get a wide range of ANF input (but weak on a per input basis) |
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For example, see McGinley et al., 2012 or Spencer et al., 2012. |
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|
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|
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""" |
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add_table_data( |
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"convergence_range", |
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row_key="pre_type", |
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col_key="post_type", |
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species="mouse", |
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data=mouse_convergence_range, |
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) |
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# -------------------------------------------------------------------------------------------- |
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guineapig_convergence = u""" |
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|
|
Convergence defines the average number of presynaptic cells of a particular |
|
type (rows) that synapse onto a single postsynaptic cell of a particular |
|
type (columns). |
|
This connectivity matrix is currently incomplete. |
|
Note: Bushy and pyramidal cells are known to have no (or very few) |
|
collaterals within the CN, and so they are not listed as presynaptic cells in |
|
this table. Octopus cells have collaterals (including in granule cell domains), |
|
and should be added to this table when more data are available (Golding et al., |
|
J. Neurosci. 15: 3138, 1995) |
|
|
|
This table is just a guess... using mouse data... |
|
|
|
---------------------------------------------------------------------------------------------- |
|
bushy tstellate dstellate octopus pyramidal tuberculoventral mso |
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sgc 3.3±0.6 [2] 6.5±1.0 [2] 35±0 [3] 60±0 [2] 48±0 [5] 24±0 [5] 0 |
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bushy 0 0 0 0 0 0 12 [8] |
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dstellate 7 [1] 20 [1] 3 [1] 0 [4] 15 [5] 15 [5] 0 |
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tstellate 0 [6] 0 [6] 0 [6] 0 [6] 0 [6] 0 [6] 0 |
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tuberculoventral 6 6 0 0 [4] 21 [5] 0 [7] 0 |
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pyramidal 0 0 0 0 0 0 0 |
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---------------------------------------------------------------------------------------------- |
|
|
|
[1] Guesses based on Campagnola & Manis 2014 (using mouse data on guinea pig cells) |
|
|
|
[2] Cao, X. & Oertel, D. (2010). Auditory nerve fibers excite targets through |
|
synapses that vary in convergence, strength, and short-term plasticity. |
|
Journal of Neurophysiology, 104(5), 2308–20. |
|
Xie and Manis (unpublished): max EPSC = 3.4 ± 1.5 nA with ~0.3 nA steps |
|
(Cao and Oertel, 2010) = ~11 AN inputs. However neither we nor Cao and Oertel |
|
see that many clear steps in the responses, so use lower bound. |
|
|
|
[3] Lower bound based on estimates from unpublished data Xie and Manis (2017) |
|
Assumptions: No discernable step sizes when increasing shock intensity |
|
at ANFs in radiate multipolars (dstellate) |
|
Measured: 0.034 ± 15 nA sEPSC @ -70 mV |
|
Measured: Maximal current from AN stim = 1.2 ± 0.7 nA @ -70 mV |
|
Assuming that each AN provides 1 input, then N = ~35 |
|
|
|
[4] Octopus cells are devoid of inhibitory input (Golding et al., J. Neurosci., 1995) |
|
|
|
[5] Convergence from Hancock and Voigt, Ann. Biomed. Eng. 27, 1999 and Zheng and Voigt, |
|
Ann. Biomed. Eng., 34, 2006. Numbers are based on models for cat and gerbil, |
|
respectively. Adjusted to 1/2 to avoid overexciting TV cells in network model. |
|
|
|
[6] tstellate cells have collaterals within the CN. It has been proposed that they |
|
provide auditory-driven input to the DCN (Oertel and Young, ), and also synapse |
|
within the VCN (Oertel, SFN abstract). These parameters may need to be adjusted |
|
once the convergence and strength is known. |
|
|
|
[7] In the models of Hancock and Voigt (1999) and Zheng and Voigt (2006), the TV cells |
|
have no connections with each other. However, Kuo et al. (J. Neurophysiol., 2015) |
|
did see connections between pairs of TV cells in the mouse. |
|
|
|
[8] Bushy convergence to MSO is a guess |
|
""" |
|
|
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add_table_data( |
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"convergence", |
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row_key="pre_type", |
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col_key="post_type", |
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species="guineapig", |
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data=guineapig_convergence, |
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) |
|
|
|
|
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guineapig_convergence_range = u""" |
|
|
|
The convergence range table describes, for each type of connection from |
|
presynaptic (rows) to postsynaptic (columns), the variance in frequency of |
|
presynaptic cells relative to the postsynaptic cell. |
|
|
|
All values are expressed as the sigma for a lognormal distribution scaled to |
|
the CF of the postsynaptic cell. |
|
|
|
*** This table is just a guess - using data from mouse... **** |
|
|
|
------------------------------------------------------------------------------------------------------- |
|
bushy tstellate dstellate octopus pyramidal tuberculoventral mso |
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sgc 0.05 [1] 0.1 [1] 0.4 [1] 0.5 [5] 0.1 [1] 0.1 [1] 0 |
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bushy 0 0 0 0 0 0 0.05 [6] |
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dstellate 0.208 [2] 0.347 [2] 0.5 [1] 0 0.2 [1] 0.2 [1] 0 |
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tstellate 0.1 [4] 0.1 [4] 0 0 0 0 0 |
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tuberculoventral 0.069 [3] 0.111 [3] 0 0 0.15 [1] 0 0 |
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pyramidal 0 0 0 0 0 0 0 |
|
-------------------------------------------------------------------------------------------------------- |
|
|
|
[1] Guess based on axonal / dendritic morphology. |
|
|
|
[2] Calculated from Campagnola & Manis 2014 fig. 7C (Using mouse data on guinea pig cells) |
|
Distribution widths are given in stdev(octaves), so we multiply by ln(2) to |
|
get the sigma for a lognormal distribution. |
|
DS->Bushy: ln(2) * 0.3 = 0.208 |
|
DS->TStellate: ln(2) * 0.5 = 0.347 |
|
|
|
[3] Calculated from Campagnola & Manis 2014 fig. 9C (Using mouse data on guinea pig cells) |
|
Distribution widths are given in stdev(octaves), so we multiply by ln(2) to |
|
get the sigma for a lognormal distribution. |
|
TV->Bushy: ln(2) * 0.10 = 0.069 |
|
TV->TStellate: ln(2) * 0.16 = 0.111 |
|
|
|
[4] Guess based on very limited information in Campagnola & Manis 2014 fig. 12 |
|
|
|
[5] Octopus cells get a wide range of ANF input (but weak on a per input basis) |
|
For example, see McGinley et al., 2012 or Spencer et al., 2012. |
|
|
|
[6] MSO convergence from bushy cells is a guess. |
|
|
|
""" |
|
|
|
add_table_data( |
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"convergence_range", |
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row_key="pre_type", |
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col_key="post_type", |
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species="guineapig", |
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data=guineapig_convergence_range, |
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)
|
|
|