Dendritica
Version 1.0
9 February 2001
Philipp Vetter, Arnd Roth and Michael Häusser
____________________________________________________________________
Table of
contents
1. General Introduction.................................................................................................................... 2
1.1 Directory structure................................................................................................................. 2
2. Getting Started............................................................................................................................. 4
2.1 A sample session.................................................................................................................... 4
2.2 Options available from the GUI.............................................................................................. 4
2.3 On-line help........................................................................................................................... 5
2.4 Basic commands for running simulations............................................................................... 6
2.5 What happens when loading a cell.......................................................................................... 6
2.6 What happens during simulations........................................................................................... 6
3. Batch Simulations........................................................................................................................ 8
3.1 Examples............................................................................................................................... 8
3.2 How batch simulations are done............................................................................................. 8
4. Batch Analysis............................................................................................................................. 9
4.1 A sample session.................................................................................................................... 9
4.2 Basic commands................................................................................................................... 10
4.3 Settings................................................................................................................................ 10
4.4 What happens during correlation analysis............................................................................. 11
4.5 List of functional parameters................................................................................................ 12
4.6 List of geometric parameters................................................................................................ 13
5. Appendix 1: Modifications to NEURON 4.1.1........................................................................... 14
6. Appendix 2: List of functions.................................................................................................... 15
Dendritica
is a program package for relating dendritic geometry and signal propagation. The programs are based on those used for the simulations
described in the following paper:
Vetter, P., Roth,
A. & Häusser, M. (2001).
Action potential propagation in dendrites depends on dendritic morphology. Journal
of Neurophysiology, 85: 926-937.
Dendritica can functionally be divided into three main parts:
·
interactive
morphological analysis and electrophysiological simulation of single cells
·
automated
batch simulations across a set of morphologies using the same simulation
parameters
·
automated
analysis of batch simulation runs
Dendritica
requires NEURON 4.1.1 with some modifications described in Appendix 1. It was
tested for NEURON 4.1.1 on Linux and SGI IRIX. Some
modifications to the Dendritica code
may be necessary in order to run it on older or newer versions of NEURON.
We are very grateful to Muki Rapp, Diana Smetters, Nelson Spruston, Greg Stuart, and the contributors to the Duke-Southampton Neuronal Morphology Archive (accessible via http://www.neuro.soton.ac.uk) for allowing us to use their neuronal reconstructions for this project. We also thank Alain Destexhe (Destexhe@iaf.cnrs-gif.fr) and Zach Mainen (mainen@cshl.org) for providing NEURON code. Please note that while the programs in Dendritica are freely available, they are protected by the GNU public licence, and we request that you acknowledge us if you use the programs for a publication. If you require further information, please do not hesitate to contact any of the authors: Philipp Vetter (p.vetter@ucl.ac.uk), Arnd Roth (roth@mpimf-heidelberg.mpg.de), or Michael Häusser (m.hausser@ucl.ac.uk).
The directory structure is defined automatically when you untar the package. The structure must be respected for most of the functions to work properly.
The directory dendritica-1.0 contains all files. There are three subdirectories:
batch_back/
batch_forward/ batch_forward2/
indicating different types of simulation runs, i.e. looking a backpropagating action potentials and forward propagating action potentials. The structure of the subdirectories is identical, however.
batch_back/back:
aphalf.hoc gui.hoc
batch1.hoc help.hoc
batch2.hoc impedance.hoc
batch3.hoc init.hoc
batchrun mod/
bp neuronprefs.hoc
dendspike_p21 output.hoc
electrophysiology.hoc parse.hoc
figures.hoc referenceAP_p18@200um_act0
forward.hoc settings.hoc
geometry.hoc statistics.hoc
graphics.hoc
The *.hoc files contain the code for the NEURON interpreter. It is split into several files according to what the procedures/functions do. The directory mod/ contains all mod files necessary to create the special executable of NEURON. The mod files for the simulations are in the subdirectory kvz_naz. dendspike_p21 and referenceAP_p18@200um_act0 are saved waveforms that can be played in during simulations.
batch_back/data:
act0/ cells/ geometry/
act0 contains simulation results that depend on the active model used, while geometry contains simulations results that are independent. cells contains the morphologies of all the cells used.
batch_back/neuron_output:
This contains ascii files with correlation analysis from a batch run.
Most of the data presented in the paper are directly accessible through the graphical user interface (GUI). (Note that the optimization routine to find halfdecay_max is an exception).
·
To
create the program special
go to dendritica-1.0/batch_back/back/mod/kvz_naz/
·
To
create special type
>nrnivmodl
·
Move
special to dendritica-1.0/batch_back/back/, then load the GUI with
>special
gui.hoc -
Dialog
box: Welcome to Progagation Geometry [Load Cell] [Statistics]
·
Choose
[Load
Cell]
Dialog
box: Please pick a neuron and an active model [Neuron] [Conductances]
·
Specify
Neuron [Nigra]->[Nigra2], and Conductance [standard
conductances]
(act0 is the setting used in the
paper), and then [Accept].
The Morphology is loaded, and subsequently the panels Electrophysiology and Main (see below) are called.
[Voltage Clamp] runs a Voltage clamp simulation with the Electrode standardly located at the soma. This takes about a minute on a PentiumII, depending also on the morphology being simulated. The position can be changed manually by clicking on [Location]. The size of the waveform can be changed by entering a value under [scaling]. The standard waveform is somatic AP (p18), but others can be chosen from the pull-down menu [waveform].
[Current Clamp] clamps a constant current, standardly at the soma. The electrode location can be changed manually using [Location]. The magnitude of the current can be specified by changing [Amplitude].
[Synapse] simulates a synapse. The parameters and location of the synapse can be altered by clicking on [Location] and/or [gmax].
[Input Resistance] calculates the input resistance at the soma.
[g_na threshold] calculates the Na-channel density for full backpropagation. This simulation can take >30 minutes!
·
Press
[Voltage
Clamp]. After
the simulation is over, 4 figures are plotted:
(1)
Voltage
traces at soma, node and dendrite
(2)
The
AP amplitude as a function of distance from the soma
(3)
Simulation
settings
(4)
Plot
of rate of change of peak voltage as a function of distance from the soma
The
same plots are obtained when simulating [Current
Clamp] or [Synapse].
[Load Neuron]
[Clear Screen]
[Graphs]
->[New Graph]
->[Which Sections]
->[Which Lengths]
->[Simulation]
->[Geometric Values]
->[Functional Values]
->[Simulation X against distance]
->[Geometric individual]
->[Impedance individual]
[Other Panels]
->[Electrophysiology]
->[Statistics]
->[Channels]
->[Simulation settings]
->[Geometry]
[Miscellaneous]
->..
[Quit]
·
Choose [Graphs]->[Which
Sections]->[all]
to plot figures (2) & (4) with data from all segments of the Morphology.
·
Choose
[Graphs]->[Which
Lengths]->[electrotonic]
to plot
figures (2) & (4) in electrotonic space (X-axis!).
·
Choose
[Other
Panels]->[Simulation settings]
to call up a
panel allowing to change simulation duration, and time step.
·
Choose
[Other
Panels]->[Conductances]
to call up a
panel which allows setting of the active membrane properties.
·
To
re-run the simulation, simply press [Voltage Clamp] in the panel Electrophysiology. Units as in the paper.
·
Choose
[Other
Panels]->[Geometry]
to call up a
panel which allows the Axon to be removed [Remove Axon] or added to the morphology [Connect Axon].
·
[Graphs]->[Geometric Values] Plots 5 figures that have been calculated
in a batch simulation (see next section)
(1)
Branchpoint
and Termination histogram as a function of distance from the soma
(2)
Cumulative
membrane area as a function of distance from the soma
(3)
Rate
of change in membrane against distance from the soma
(4)
Rall
ratio distribution of branchpoints (smoothed)
(5)
number of
sections at a given distance from the soma.
An on-line help can be accessed from the command line. All functions and procedures of the package can be listed with the command
oc>hlp()
parse.hoc
get()
get_somadist()
connect_axon()
...
The listing is sorted according to the .hoc files the functions and procedures are defined in. To get more information about a particular function, e.g. the function get, type
oc>hlp(“get”)
get cell $s1
use ActiveModel $s2
load data if numarg=3
There are four basic commands to run simulations from the command line (see hlp() for details)
·
get() loads
a morphology, it’s simulation results, gets it ready for simulations
·
sim() runs
a simulation
·
fig() plots
vectors
·
spaceplot() dumps a spaceplot on disk
get() loads morphologies from ../data/cells/<name of cell>, specifies name and spine_density in neuronprefs.hoc (structure MyCell) inserts passive membrane properties and channels parse.hoc, then sets the parameters as specified in settings.hoc. To facilitate analysis, the morphology is split into soma and dendrites (note Purkinje cells have two types of dendrites), and SectionLists are specified in parse.hoc accordingly.
dist_switch()
if (n == 1) distlist =
trunk
if (n == 2) distlist =
all
if (n == 3) distlist =
branchpoints
if (n == 4) distlist =
terminations
if (n == 5) distlist =
branchpt_noend
if (n == 6) distlist =
all_noend
Simulation results (calculated previously) are loaded from ../data/act0/ and ../data/geometry” into vectors. These vectors can be printed using pt(<vectorname>), or plotted using fig(<vectorname>). Vectors can be plotted against each other as fig(<vectorx>,<vectory>) (see hlp(“fig”)).
Most functions to do with simulations are in electrophysiology.hoc (see hlp() for details). Simulations come in three flavours - voltage clamp/current clamp/synapse, which is set by the flag simMode. sim() brings the cell to resting potential with rest(), then inserts the appropriate PointProcess. The unused PointProcesses are parked on a dummy section. sim then calls simcore() which is equivalent to run(). Because some values, like the AP half-width require knowledge of the AP-waveform, simcore() has to be called twice, so that these values can be calculated.
To be able to plot them, type
>sim_calc()
which creates the following vectors that can be plotted against distance from the soma.
·
vpk
- peak voltage
·
amp
- AP amplitude
·
vmax
- maximum velocity
·
plat
- peak latency
·
olat
- onset latency
·
half
- half distance
·
dvdr
- spatial derivative of peak voltage
e.g.
>sim()
>dist_switch(2) // all sections [optional]
>L_switch(0) // physical lengths
[optional]
>sim_calc()
>fig(dist,vpk)
Batch simulations allow for the automated generation and saving of simulation results across a wide range of morphologies using the same set of simulation parameters. Because these calculations are computationally intensive, it is more efficient to invoke batch() without using the GUI. Simulation runs take >24 hours on a PentiumII 450 MHz.
>batch(17,act0)
performs all the calculations in conjuction with action potential backpropagation, using the standard active model “act0”.
>batch(18,act0)
performs all the calculations when the action potential is generated at a dendritic location 200 um from the soma.
>batch(19,act0)
performs all the calculations when the action potential is generated at the dendritic location from where the action potential has the greatest halfdecay distance.
The procedure batch() is a loop which applies a function to all cells in turn. The specifics of this are defined in output.hoc Basically, calculations done in electrophysiology.hoc, geometry.hoc and impedance.hoc are saved as numbers or vectors in the directories ../data/act0 and ../data/geometry. The convention is that the directory name is the same as the vector, and the filename is the same as that of morphological data of the cell in ../data/cells.
The results of the batch simulations can be analysed using the graphical user interface.
·
Go
to directory dendritica-1.0/batch_back/back/ and type
>special
gui.hoc -
Dialog
box: Welcome to Progagation Geometry [Load Cell] [Statistics]
·
Choose
[Statistics]
Dialog
box: Select dataset to analyse
[Conductances]
[]
equivalent
[]
backpropagation
[]
forward200
[]
forwardhdecay
·
Select
[Conductances]->[standard]
·
Select
[x]
backpropagation
·
Press
[Load]
The simulation results are loaded into memory, and the panels Main and Statistics are opened
[Get_Data][Legend]
[Average][Single][Double][Triple][]Powers
[Y]
[X1]
[X2]
[X3]
·
Choose
[Y]->[1]->[nathresholdvclamp]
·
Press
[Average]
This does 3 things
(1)
plots
a bar chart with cell-type averaged Na thresh values under voltage clamp
(2)
prints
numerical values on command line
(3)
saves
numerical values in ascii in
dendritica-1.0/batch_back/neuron_output/nathresholdvclamp
·
Choose
[X1]->[3]->[d2area_max]
·
Press
[Single]
·
Press
[Legend] This correlates the maximum
rate of rise in membrane area as a function of distance from the soma with
nathresholdvclamp and shows a legend colour-coding the cell types. Again, 3
things are done
(4)
correlation
plot
(5)
numerical
values on command line
(6)
numerical
values saved in
/neuron_output/nathresholdvclamp
vs branchpoints_num (act0)
·
Choose
[]
Powers
·
Press
[Single]
This does the
same as before, but maximizes the correlation nathresholdvclamp and
d2area_max^exponent, by varying the exponent.
·
Choose
[X2]->[3]->[diam_mean]
·
Press
[Double]
This maximizes the correlation between nathresholdvclamp and (d2area_max^a * diam_mean^b)
·
Press
[Clear
Screen]
·
Choose
[X1]->[geometric]
·
Deselect
(optional) Powers
·
Press
[Single]
This plots the 6 best correlations of geometric parameters against
nathresholdvclamp, and plots a ranked list of correlations on the command line
·
Press
[Clear
Screen]
·
Type
>make_figures()
This creates all the average and correlation plots shown in
the paper.
·
Type
>multi_correlation()
This
will save all good single and multiple correlations into the file
dendritica-1.0/batch_back/neuron_output/backpropagation
There are six key commands for ANALYSIS/STATISTICS
(1)
get_data() loads
simulation results for the whole batch of cells
(2)
averages() prints/plots
cell-type average for any parameter
(3)
cplot() correlates
two parameters with each other
(4)
single_corr()
correlates one parameter with all geometric parameters
(5)
single_corrf() correlates one parameter with all
functional parameters
(6)
writevecs() writes vectors to disk
FLAGS
that have to be set (use before calling get()):
equiv 1=
equivalent cylinder mode
hdecay 1= morphology is cut in two,
where the halfdecay distance is maximal; distal
part
removed
forward 1= morphology cut in two 200 um from soma, distal part removed
simMode 0= do voltage clamp when sim() is called
1=
do current clamp when sim() is called
3=
do synapse when sim() is called
electrotonicL 0= physical lengths
1= electrotonic lengths
During correlation analysis, all simulation results are read from disk into the vector
data[i][j][k]
·
i
={0,1,2} and specifies, respectively, a
functional,physically-geometric,electrotonically-geometric parameter
·
j
={0..30} for the different parameters
·
k
={0,1,2} 0 = parameter (normal), 1 =exp(parameter), 2 = ln(parameter)
It’s a nuisance to specify one vector with three numbers, so there is a one-number shorthand
1000*i + 100*k + j {if i==0 add 3000 }
dissect() turns shorthand into ci,cj,ck, antidissect() does the opposite. Because they are all vectors they can be plotted and manipulated as mentioned above.
To get averages of a parameter for a given cell-type
>averages(3014) // gets nathreshold (voltage clamp
mode) averages
N.B. This writes the numerical values into a correctly named file
../neuron_output/nathesholdvclamp
To make the correlations, the appropriate data[][][] vectors are copied into vecx and vecy, and Rcorrelation() is applied. To correlate two parameters
>cplot(3014,1000)
N.B. This writes the numerical values into a correctly named file in ../neuron_output/nathresholdvclamp_vs_area_max_act0
N.B.II All such data relevant for the figures is generated automatically using make_figures()
Many correlations are possible (just loop through the indices i,j,k)
and in order to make sense of the data (single_corr()/single_corrf(),double_corr(). To make the data more easy to read, they are ranked according to their correlation coefficient in good_corr().
To look at a mix of these correlations (with and without powers | normal or equivalent cable geometries etc)
r =
distance from soma
Dr = incremental distance
|
Parameter st_intensity |
# 3001 |
Description
Current needed to elicit a nodal AP in the absence of
somatic/dendritic sodium channels |
|
Nathreshold |
3000 |
g_na that leads to a depolarization >0mV in all sections
during current clamp at st_intensity |
|
Nathresholdvclamp |
3014 |
g_na
that leads to a depolarization >0mV in all sections during voltage clamp
with AP waveform |
|
nathresholdvclamp2 |
3021 |
g_na
that leads to a depolarization >0mV in terminal sections during voltage
clamp with AP waveform |
|
AP200 |
3010 |
AP
amplitude 200 um from soma / AP amplitude at soma |
|
AP200_pass |
3011 |
AP amplitude 200 um from soma / AP amplitude at soma (g_na = 0) |
|
AP200_half |
3016 |
Sigmoidal fit of
AP200 = f(g_na) AP200 = AP200_basis + AP200_range/ { 1+exp[-(g_na –
AP200_half)/AP200_steep)]} |
|
AP200_steep |
3017 |
See above |
|
AP200_range |
3018 |
See
above |
|
AP200_basis |
3019 |
See
above |
|
Aphalf |
3012 |
Distance
from soma at which AP amplitude has decayed to 50% |
|
APhalf_pass |
3013 |
Distance
from soma at which AP amplitude has decayed to 50% (g_na=0) |
|
input_resistance |
3015 |
Input
resistance at soma |
|
Rfwd_min |
3026 |
minimum
somatofugal input resistance: Cut
morphology in half at a given point, and measure the input resistance at the
end with the somatofugal portion of the morphology |
|
Rfwd_max |
3027 |
Maximum
somatofugal input resistance |
|
Zfwd_min |
3022 |
minimum
somatofugal input impedance (f=200 Hz) |
|
Zfwd_max |
3023 |
Maximum
somatofugal input impedance (f=200 Hz) |
|
Rmismatch_peak |
3002 |
Cut
morphology in half at a given point Measure
resting input resistance at both new ends. Mismatch
is defined as the ratio of somatopetal/somatofugal input resistance. =>
peak value of this mismatch |
|
Zmismatch_peak |
3003 |
Same
as above, but measuring input impedance at 200 Hz |
|
aRmismatch_peak |
3004 |
Same
as Rmismatch_peak, but measuring resistance at time, when the peak of the
action potential has just reached the point of measurement. |
|
aZmismatch_peak |
3005 |
Analogous |
|
Rmismatch_mean |
3006 |
Same
calculations as above, but take the mean over all points instead of peak. |
|
Zmismatch_mean |
3007 |
Analogous |
|
aRmismatch_mean |
3008 |
Analogous |
|
aZmismatch_mean |
3009 |
Analogous |
|
dZfwd_max |
3024 |
Maximum DZfwd/ Dr |
|
dZfwd_min |
3025 |
Minimum DZfwd/ Dr |
|
dRfwd_max |
3028 |
Maximum DZfwd/ Dr |
|
dRfwd_min |
3029 |
Maximum DZfwd/ Dr |
|
aZfwd_min |
3030 |
Same
as Zfwd_min, but calculations done when action potential has just reached the
point at which the cut is made. |
|
aZfwd_max |
3031 |
Analogous |
|
daZfwd_max |
3032 |
Analogous |
|
daZfwd_min |
3033 |
Analogous |
|
aRfwd_min |
3034 |
Analogous |
|
aRfwd_max |
3035 |
Analogous |
|
daRfwd_max |
3036 |
Analogous |
|
daRfwd_min |
3037 |
Analogous |
|
cZfwd_min |
3038 |
Minimum
of DZfwd/ (Dr × Zfwd) over morphology |
|
cZfwd_max |
3039 |
Maximum
of DZfwd/ (Dr × Zfwd) over morphology |
|
cRfwd_min |
3040 |
Minimum
of DRfwd/ (Dr × Rfwd) over morphology |
|
cRfwd_max |
3041 |
Maximum
of DRfwd/ (Dr × Rfwd) over morphology |
|
caZfwd_min |
3042 |
Minimum
of DZfwd/ (Dr × Zfwd) over morphology when AP has just reached point |
|
caZfwd_max |
3043 |
Maximum
of DZfwd/ (Dr × Zfwd) over morphology when AP has just reached point |
|
caRfwd_min |
3044 |
Minimum
of DRfwd/ (Dr × Rfwd) over morphology when AP has just reached point |
|
caRfwd_max |
3045 |
Maximum
of DRwd/ (Dr × Rfwd) over morphology when AP has just reached point |
|
PARAMETER branchpoints_num |
# 1003 |
DESCRIPTION Number of branchpoints |
|
distance_max |
1006 |
Maximum r |
|
area_max |
1002 |
Total membrane area (spine corrected) |
|
taper_mean |
1010 |
Mean taper D(diameter)/ Dr in the somatofugal direction |
|
darea_max |
1000 |
Maximum
D(membrane area)/ Dr |
|
darea_maxdist |
1001 |
r
at which maximum D(membrane area)/ Dr is reached |
|
dAdr_relmax |
1012 |
First relative maximum in the change of membrane area after the first minimum change of
membrane area as a fxn of distance from soma; these values are calculated
semi-automatically |
|
dAdr_ratio |
1011 |
dAdr_relmax / preceding minimum change in membrane area as a fxn
of distance from soma; these values are calculated semi-automatically |
|
d2area_max |
1013 |
Maximum
rate of change in D(membrane area)/ Dr as a function of distance from the soma |
|
d2area_maxdist |
1014 |
Distance
from the soma at which d2area_max is reached |
|
d2area_maxAr_ratio |
1015 |
At d2area_maxdist:
membrane area distal to soma/membrane area proximal to soma |
|
d2area_maxAr_percent |
1016 |
At
d2area_maxdist: 100*membrane
area distal to soma/total membrane area |
|
rallratio_mean |
1004 |
Mean
of the distribution of Rall ratios obtained from the branchpoints in the
morphology |
|
rallratio_peak |
1005 |
Peak
in the distribution of Rall-ratios obtained from the branchpoints in the
morphology |
|
sections_max |
1007 |
Maximum
number of sections at a given distance from the soma |
|
sections_maxdist |
1008 |
r
at which sections_max |
|
sections_mean |
1009 |
Mean
number of sections at all r |
|
diam_mean |
1017 |
Mean
dendritic diameter |
|
branchdensity |
1018 |
Mean
distance between branchpoints |
|
branchdensityII |
1019 |
Number
of branchpoints / total length of dendritic sections |
|
branchdensityII_noend |
1023 |
Number
of branchpoints / total length
of non-terminal dendritic sections |
|
diamratio_peak |
1020 |
Peak of the distribution of diamter ratios at branchpoints given
by Sdaughter branches / parent branch |
|
diamratio_mean |
1021 |
Mean of the above distribution |
|
diamratio_noend_peak |
1024 |
Same as diamratio_peak but leaving out terminal branchpoints |
|
diamratio_noend_mean |
1025 |
Same as diamratio_mean but leaving out terminal branchpoints |
|
mean_stem_dendrite_diam |
1026 |
Mean diameter of dendrites branching off from soma |
|
rallratio_noend_peak |
1027 |
Same as rallratio_peak, but omitting terminal branchpoints |
|
rallratio_noend_mean |
1028 |
Same as rallratio_mean, but omitting terminal branchpoints |
|
deq_relmax |
2014 |
Equivalent to dAdr_relmax in the equivalent cable representation |
|
deq_ratio |
2015 |
Equivalent to dAdr_ratio in the equivalent cable representation |
|
ddeq_max |
2016 |
Equivalent to d2_area_max in the equivalent cable representation |
|
ddeq_maxdist |
2017 |
Equivalent to d2_area_maxdist in the equivalent cable
representation |
|
ddeq_maxAr_ratio |
2018 |
Equivalent to d2_area_maxAr_ratio in the equivalent cable representation |
|
adarea_max |
2000 |
darea_max in
electrotonic space |
|
adarea_maxdist |
2001 |
darea_maxdist in electrotonic space |
|
adistance_max |
2002 |
distance_max in electrotonic space |
|
asections_max |
2003 |
sections_max in electrotonic space |
|
asections_maxdist |
2004 |
sections_maxdist in electrotonic space |
|
asections_mean |
2005 |
sections_mean in electrotonic space |
|
ataper_mean |
2006 |
taper_mean in electrotonic space |
|
adiam_mean |
2011 |
diam_mean in electrotonic space |
|
abranchdensity |
2007 |
branchdensity in electrotonic space |
|
abranchdensityII |
2008 |
branchdensityII in electrotonic space |
|
abranchdensityII_noend |
2010 |
branchdensityII_noend in electrotonic space |
|
adeq_max |
2012 |
deq_max in electrotonic space |
|
adeq_maxdist |
2013 |
deq_maxdist in electrotonic space |
To run all parts of Dendritica successfully, the following modifications to the NEURON source code are required.
diff -r nrn.new/src/ivoc/vector.c nrn.old/src/ivoc/vector.c
65,66c65,66
< // #define BYTEHEADER int BYTESWAP_FLAG=0;
< // #define BYTESWAP(_X__,_TYPE__)
• #define BYTEHEADER int BYTESWAP_FLAG=0;
• #define BYTESWAP(_X__,_TYPE__)
68,69c68,69
< #if 1
< // #include <sys/isa_defs.h>
• #if 0
• #include <sys/isa_defs.h>
Only in nrn.new/src/ivoc: vector.c.byteswap
Only in nrn.new/src/ivoc: vector.c.orig
diff -r nrn.new/src/nrnoc/cabcode.c nrn.old/src/nrnoc/cabcode.c
48,49c48
< #define NSECSTACK 10000
< /* A.R. 28.12.1998 */
• #define NSECSTACK 20
Only in nrn.new/src/nrnoc: cabcode.c.orig
diff -r nrn.new/src/oc/hoc_oop.c nrn.old/src/oc/hoc_oop.c
184,185c184
< #define NTYPESTACK 10000
< /* A.R. 28.12.1998 */
• #define NTYPESTACK 30
218,219c217
< #define NTEMPLATESTACK 10000
< /* A.R. 28.12.1998 */
• #define NTEMPLATESTACK 20
Only in nrn.new/src/oc: hoc_oop.c.orig
NEURON must be recompiled for the changes to take effect.
parse.hoc
get()
get_somadist()
connect_axon()
add_axon()
remove_axon()
insert_channels()
make_sectionlists()
isterminal()
make_distvectors()
switch()
dist_switch()
L_switch()
make_vectors()
single_vectors()
set_origin()
help.hoc
hlp()
hlpscan()
hlpfound()
fxnscan()
check()
consistency()
get_parents()
find_section()
traces()
fxarea()
sectest()
which()
electrophysiology.hoc
rest()
simcore()
sim()
initsimvclamp()
dvdr_calc()
sim_err()
sim_fit()
rinput_calc()
sim_calc()
threshold_calc()
forwardthreshold_calc()
threshold_find()
threshold()
thresh()
APdecay()
APdecay_sensitivity()
sigmoidal()
sigmoidal_calc()
scrappy()
impedance.hoc
impedance_calc()
impedance_mismatch()
switch_off_intra()
switch_on_intra()
get_children()
switch_on()
imp_calc()
impedance_check()
get_Zfwdvalues()
get_cZ()
get_APfrequencies()
cosine()
cosinefxn()
cosinefit()
forward.hoc
name_somadist()
name_halfdecay()
resize_cell()
output.hoc
batch()
calculation()
manual()
save_geometry()
save_active()
save_cable()
save_forwardmini()
save_all()
save_back()
save_fI()
save_fII()
helpme()
write_numbers()
write_nathreshold()
geometry_read()
active_read()
normforward()
equivforward()
equivforwardII()
printvectors()
printvectors_back()
printvectors_forward()
printvectors_forward2()
make_figures()
equivZfwdwrite()
statistics.hoc
get_neurondata()
add_vals()
lg()
get_data()
compare_activemodels()
c2()
c3()
c()
dissect()
antidissect()
clean()
correl_raw()
correl_func1()
correl_func2()
correl_func3()
Rcorrelation()
single_corr()
single_corrf()
double_corr()
triple_corr()
clegend()
averages()
label_list()
clabel()
Cplot()
powerplot()
cplot()
get_geomorder()
multiplot()
datalegend()
good_corr_func()
good_doublecorr()
checkit()
multi_correlation()
write_singlecorr()
neuronprefs.hoc
add_cell()
cell_name()
set_suffix()
set_spinedensity()
dendII()
dendIII()
swc_format()
make_sectionrefs()
geometry.hoc
fdistance()
fL()
segL()
mindist()
maxdist()
farea()
sectionarea()
fseg()
fbranch()
get_parent()
pbranchpoint()
nextparent()
branchpoint()
get_root()
ubranch()
get_rall()
rall_calc()
ename()
gstep()
make_dAr()
get_gdist()
geometry_calc()
mean()
div()
equivalent_calc()
spinetransform()
make_equivalent_cable()
slope_darea()
slope_deq()
dAdr_calc()
dAdr_write()
deq_calc()
deq_write()
estcore()
tap()
lintaper()
get_link()
set_electrotonic()
graphics.hoc
flip()
pt()
P()
ar()
mx()
mn()
mod()
ceil()
fig()
figlab()
clf()
hist()
gauss()
bar()
sort()
filter()
rolling()
rolling2()
roll()
writevec_el()
writeveca()
readveca()
writevec()
readvec()
writevecs()
nvectors()
nasens()
spaceplot()
show()