data = dsProbeCellProperties(model,'option1',option1,...)
This experiment is designed to probe the intrinsic properties of cells in
one or more populations. It removes all connections between cells and
populations and then runs a series of simulations delivering
hyperpolarizing and depolarizing pulses. It is designed to be used in
conjunction with the analysis function "dsCalcCellProperties" which accepts
the data array produced by this experiment and returns the
electrophysiological properties characterizing each cell's response in
the population.
Options:
'amplitudes' : numeric array of applied current amplitudes (default: -30:5:180)
units: if [I]=uA/cm2, then [amp]=pA (typical values: 0-500pA)
'membrane_area' : um, compartment surface area
'onset' : ms, time to start the applied current
'offset' : ms, time to stop the applied current
'tspan' : [beg,end], ms, simulation interval
'remove_connections_flag' (default: 1): whether to remove connections
note: if 0, the input is applied only to the first cell/compartment,
otherwise the input is applied to all cells/compartments.
Example: ...
model='dv/dt=(@current-.1*(v+70))/Cm; Cm=1; {iNa,iK}';
data=dsProbeCellProperties(model,'verbose_flag',1);
dsPlot(data(1:10));
dsPlot(data(11:20));
model='dv/dt=@current-.1*(v+70)+5*randn; {iNa,iK}';
data=dsProbeCellProperties(model,'num_repetitions',2);
Note: this function is based on the DNSim experiment "cell_pulses".
See also: dsCalcCellProperties0001 function data = dsProbeCellProperties(model,varargin) 0002 % data = dsProbeCellProperties(model,'option1',option1,...) 0003 % This experiment is designed to probe the intrinsic properties of cells in 0004 % one or more populations. It removes all connections between cells and 0005 % populations and then runs a series of simulations delivering 0006 % hyperpolarizing and depolarizing pulses. It is designed to be used in 0007 % conjunction with the analysis function "dsCalcCellProperties" which accepts 0008 % the data array produced by this experiment and returns the 0009 % electrophysiological properties characterizing each cell's response in 0010 % the population. 0011 % 0012 % Options: 0013 % 'amplitudes' : numeric array of applied current amplitudes (default: -30:5:180) 0014 % units: if [I]=uA/cm2, then [amp]=pA (typical values: 0-500pA) 0015 % 'membrane_area' : um, compartment surface area 0016 % 'onset' : ms, time to start the applied current 0017 % 'offset' : ms, time to stop the applied current 0018 % 'tspan' : [beg,end], ms, simulation interval 0019 % 'remove_connections_flag' (default: 1): whether to remove connections 0020 % note: if 0, the input is applied only to the first cell/compartment, 0021 % otherwise the input is applied to all cells/compartments. 0022 % 0023 % Example: ... 0024 % model='dv/dt=(@current-.1*(v+70))/Cm; Cm=1; {iNa,iK}'; 0025 % data=dsProbeCellProperties(model,'verbose_flag',1); 0026 % dsPlot(data(1:10)); 0027 % dsPlot(data(11:20)); 0028 % 0029 % model='dv/dt=@current-.1*(v+70)+5*randn; {iNa,iK}'; 0030 % data=dsProbeCellProperties(model,'num_repetitions',2); 0031 % 0032 % Note: this function is based on the DNSim experiment "cell_pulses". 0033 % See also: dsCalcCellProperties 0034 0035 % Experiment: input model, produces data sets for all step levels 0036 % Analysis: input data sets for all step levels, output one stat structure 0037 % per experiment call with ephys properties for each cell in each 0038 % population of the model. 0039 % 0040 % Author: Jason Sherfey, PhD <jssherfey@gmail.com> 0041 % Copyright (C) 2016 Jason Sherfey, Boston University, USA 0042 0043 % Check inputs 0044 options=dsCheckOptions(varargin,{... 0045 'target_equation','ODE1',[],... 0046 'amplitudes',-30:5:180,[],... % pA. typically: 0-500pA (0-.5nA) 0047 'membrane_area',1500,[],... % um^2. typically: 1000-2000 um2 0048 'tspan',[0 1500],[],... 0049 'num_repetitions',1,[],... 0050 'onset',250,[],... 0051 'offset',1250,[],... 0052 'equivalent_cells_flag',0,[],... % if true, only simulate one cell per pop 0053 'remove_connections_flag',1,[],... 0054 },false); 0055 0056 model=dsCheckModel(model, varargin{:}); 0057 0058 % check that amplitude=0 is present (for RMP calculation) 0059 if ~ismember(0,options.amplitudes) 0060 options.amplitudes(end+1)=0; 0061 end 0062 % convert current from pA to uA/cm^2 0063 CF = (1e-6)/(1e-8); % pA/um^2 => uA/cm^2. note: 1um2=1e-8cm2, 1pA=1e-6uA 0064 options.effective_amplitudes=CF*options.amplitudes/options.membrane_area; 0065 % options.effective_amplitudes=repmat(options.effective_amplitudes,[1 options.num_repetitions]); 0066 % options.amplitudes=repmat(options.amplitudes,[1 options.num_repetitions]); 0067 0068 % Remove connections from the model specification and regenerate the model 0069 if ~isempty(model.specification.connections) && options.remove_connections_flag 0070 specification=model.specification; 0071 specification.connections=[]; 0072 model=dsGenerateModel(specification); 0073 end 0074 0075 % Extract population info 0076 num_pops=length(model.specification.populations); 0077 pop_names={model.specification.populations.name}; 0078 0079 % Prepare list of modifications to add input pulses 0080 modifications={}; 0081 for i=1:num_pops 0082 if isfield(model.parameters,[pop_names{i} '_Cm']) 0083 modifications(end+1,:)={pop_names{i},'equations',['cat(' options.target_equation ',+pulse(t)/Cm; pulse(t)=TONIC*(t>=onset&t<=offset); monitor pulse)']}; 0084 else 0085 modifications(end+1,:)={pop_names{i},'equations',['cat(' options.target_equation ',+pulse(t); pulse(t)=TONIC*(t>=onset&t<=offset); monitor pulse)']}; 0086 end 0087 modifications(end+1,:)={pop_names{i},'onset',options.onset}; 0088 modifications(end+1,:)={pop_names{i},'offset',options.offset}; 0089 if options.equivalent_cells_flag 0090 % Reduce each population to a single cell if homogeneous 0091 modifications(end+1,:)={pop_names{i},'size',1}; 0092 end 0093 if options.remove_connections_flag==1 0094 % only add input to the first population 0095 break 0096 end 0097 end 0098 0099 % Prepare 'vary' specification to adjust pulse amplitudes in all populations 0100 % simultaneously: {'(pop1,pop2,...)','TONIC',amplitudes} 0101 objects='('; 0102 for i=1:num_pops 0103 objects=[objects pop_names{i} ',']; 0104 if options.remove_connections_flag==1 0105 % only add input to the first population 0106 break 0107 end 0108 end 0109 objects=[objects(1:end-1) ')']; 0110 vary={objects,'TONIC',options.effective_amplitudes;... 0111 objects,'repetition',1:options.num_repetitions}; 0112 0113 % apply modifications to effectively add experimental apparatus to model 0114 model=dsApplyModifications(model,modifications, varargin{:}); 0115 0116 % execute experimental protocol by varying parameters across simulations 0117 fprintf('Running experiment: %s\n',mfilename); 0118 keyvals=dsRemoveKeyval(varargin,'tspan'); 0119 data=dsSimulate(model,'vary',vary,'tspan',options.tspan,keyvals{:}); 0120 0121 % add options to data 0122 for i=1:length(data) 0123 data(i).simulator_options.experiment_options=options; 0124 end