GitHub - ModelDBRepository/95960: Dentate gyrus granule cell: subthreshold signal processing (Schmidt-Hieber et al. 2007)

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 3 Commits
cell_1		cell_1
cell_10		cell_10
cell_11		cell_11
cell_2		cell_2
cell_3		cell_3
cell_4		cell_4
cell_5		cell_5
cell_6		cell_6
cell_7		cell_7
cell_8		cell_8
cell_9		cell_9
images		images
share		share
ChangeLog.txt		ChangeLog.txt
INSTALL.txt		INSTALL.txt
README.html		README.html
asin.mod		asin.mod
dv.mod		dv.mod
gc.hoc		gc.hoc
ih.mod		ih.mod
mosinit.hoc		mosinit.hoc
spines.mod		spines.mod
synampa.mod		synampa.mod

Repository files navigation

<html><pre>
These simulations accompany the publication:

Schmidt-Hieber C, Jonas P, Bischofberger J (2007)
Subthreshold Dendritic Signal Processing and Coincidence Detection 
in Dentate Gyrus Granule Cells. J Neurosci 27:8430-8441

For installation instructions, see INSTALL.txt

Simulations have been tested using NEURON 5.9 and 6.0 under
Windows and GNU/Linux. The gnuplot script has been tested with
gnuplot 4.2 (<a href="http://www.gnuplot.info">http://www.gnuplot.info</a>).

Once the simulation starts you can click on buttons in the gui

<img src="./images/gui.png" alt="screenshot gui" width="650">

to generate selected figures in the paper:

Figure 6a
<img src="./images/screenshot6a.png" alt="screenshot 6a" width="650">

Figure 6b
<img src="./images/screenshot6b.png" alt="screenshot 6b" width="650">

Figure 6c
<img src="./images/screenshot6c.png" alt="screenshot 6c" width="650">

Figure 7ab
<img src="./images/screenshot7ab.png" alt="screenshot 7ab" width="650">

Figure 7ac
<img src="./images/screenshot7ac.png" alt="screenshot 7ac" width="650">

Figure 7d
<img src="./images/screenshot7d.png" alt="screenshot 7d" width="650">

Figure 8ab
<img src="./images/screenshot8ab.png" alt="screenshot 8ab" width="650">

Figure 8cd
<img src="./images/screenshot8cd.png" alt="screenshot 8cd" width="650">

Send bug reports and comments to
christoph.schmidt-hieber at uni-freiburg.de

Description of files:
./gc.hoc                   Starts the simulations. Requires mod files to be compiled.
./asin.mod                 arcsine function, forwarded to hoc from math.h
./spines.mod               Introduces spine area scale factor as a range variable
                           (scale_spines).
                           Optionally, spine counts can be used as a range variable
                           as well (count_spines).
./synampa.mod              Synaptic conductance change with a biexponential time course.
./share/calcSpines.hoc     Calculate spine area scale factor from spine counts. Corrects
                           for spines hidden behind the shaft in 2D projections.
./share/config.hoc         Simulation configuration settings.
./share/controlpanel.hoc   Main control panel allowing cell and figure selection.
./share/figures.hoc        Procedures reproducing figures.
./share/fixnseg.hoc        d_lambda rule implementation.
./share/genutils.hoc       Some general-purpose routines.
./share/spine.hoc          Creates a spine, consisting of a neck (spine[0]) and a
                           head (spine[1])
./share/template.plt       Template script file for creating a gnuplot script that
                           will show a 3D plot as in figure 6D.
./cell_x/membrane.hoc      Loads cell morphology and connections, initializes spines,
                           inserts passive membrane properties. Uses a class "cell_x"
                           so that you can easily toggle between cells or use multiple
                           objects for network simulations.
./cell_x/morpho.hoc        Loads morphology and spines without making use of a class.
                           Intended for standalone use of cells.
./cell_x/morpho.txt        Coordinates and diameters of 3D points as plain text. Needed
                           by membrane.hoc to load 3D morphology from a procedure.

20071005
Cell templates now adhere to the "NetworkReadyCell" syntax - fixed some minor bugs. Schmidt-Hieber.

20170328
* Added a new cell (cell_9) and an artificial cell (cell_10) that were not
  part of the original 2007 publication.
* Added CA1 PC model (cell_11) for consistency. See
  Golding NL, Mickus TJ, Katz Y, Kath WL, Spruston N (2005)
  Factors mediating powerful voltage attenuation along CA1 pyramidal neuron
  dendrites. J Physiol 568:69-82.
  To run the original simulations as shown in the paper, use the original model from
  <a href="https://www.janelia.org/sites/default/files/Attenuation.zip">https://www.janelia.org/sites/default/files/Attenuation.zip</a>