Index A | B | C | D | F | G | H | I | L | M | N | O | P | R | S | T | U | V | W | X | Y | Z A add_self_to_plot() (cleosim.electrodes.Probe method) (cleosim.InterfaceDevice method) (cleosim.opto.OptogeneticIntervention method) add_signals() (cleosim.electrodes.Probe method) assign_coords() (in module cleosim.coordinates) assign_coords_grid_rect_prism() (in module cleosim.coordinates) assign_coords_rand_cylinder() (in module cleosim.coordinates) assign_coords_rand_rect_prism() (in module cleosim.coordinates) assign_coords_uniform_cylinder() (in module cleosim.coordinates) B brian_objects (cleosim.electrodes.Signal attribute) (cleosim.InterfaceDevice attribute) (cleosim.Recorder attribute) (cleosim.recorders.GroundTruthSpikeRecorder attribute) (cleosim.recorders.RateRecorder attribute) (cleosim.recorders.VoltageRecorder attribute) (cleosim.stimulators.StateVariableSetter attribute) (cleosim.visualization.VideoVisualizer attribute) C ChR2_four_state (in module cleosim.opto) cleosim module cleosim.coordinates module cleosim.electrodes module cleosim.opto module cleosim.processing module cleosim.recorders module cleosim.stimulators module cleosim.utilities module cleosim.visualization module CLSimulator (class in cleosim) compute() (cleosim.processing.ConstantDelay method) (cleosim.processing.Delay method) (cleosim.processing.GaussianDelay method) compute_output() (cleosim.processing.FiringRateEstimator method) (cleosim.processing.PIController method) (cleosim.processing.ProcessingBlock method) concat_coords() (in module cleosim.electrodes) connect_to_neuron_group() (cleosim.electrodes.MultiUnitSpiking method) (cleosim.electrodes.Probe method) (cleosim.electrodes.Signal method) (cleosim.electrodes.SortedSpiking method) (cleosim.electrodes.Spiking method) (cleosim.electrodes.TKLFPSignal method) (cleosim.InterfaceDevice method) (cleosim.opto.OptogeneticIntervention method) (cleosim.recorders.GroundTruthSpikeRecorder method) (cleosim.recorders.RateRecorder method) (cleosim.recorders.VoltageRecorder method) (cleosim.stimulators.StateVariableSetter method) (cleosim.visualization.VideoVisualizer method) ConstantDelay (class in cleosim.processing) coords (cleosim.electrodes.Probe attribute) cutoff_probability (cleosim.electrodes.MultiUnitSpiking attribute) (cleosim.electrodes.SortedSpiking attribute) (cleosim.electrodes.Spiking attribute) D default_blue (in module cleosim.opto) default_value (cleosim.Stimulator attribute) (cleosim.stimulators.StateVariableSetter attribute) Delay (class in cleosim.processing) delay (cleosim.processing.FiringRateEstimator attribute) (cleosim.processing.ProcessingBlock attribute) F FiringRateEstimator (class in cleosim.processing) FourStateModel (class in cleosim.opto) G GaussianDelay (class in cleosim.processing) generate_Animation() (cleosim.visualization.VideoVisualizer method) get_ctrl_signal() (cleosim.IOProcessor method) (cleosim.processing.LatencyIOProcessor method) get_orth_vectors_for_v() (in module cleosim.utilities) get_state() (cleosim.CLSimulator method) (cleosim.electrodes.MultiUnitSpiking method) (cleosim.electrodes.Probe method) (cleosim.electrodes.Signal method) (cleosim.electrodes.SortedSpiking method) (cleosim.electrodes.Spiking method) (cleosim.electrodes.TKLFPSignal method) (cleosim.Recorder method) (cleosim.recorders.GroundTruthSpikeRecorder method) (cleosim.recorders.RateRecorder method) (cleosim.recorders.VoltageRecorder method) GroundTruthSpikeRecorder (class in cleosim.recorders) H half_detection_radius (cleosim.electrodes.MultiUnitSpiking attribute) (cleosim.electrodes.SortedSpiking attribute) (cleosim.electrodes.Spiking attribute) I i (cleosim.electrodes.MultiUnitSpiking attribute) (cleosim.electrodes.SortedSpiking attribute) (cleosim.electrodes.Spiking attribute) i_probe_by_i_ng (cleosim.electrodes.MultiUnitSpiking attribute) (cleosim.electrodes.SortedSpiking attribute) (cleosim.electrodes.Spiking attribute) init_for_probe() (cleosim.electrodes.Signal method) (cleosim.electrodes.TKLFPSignal method) init_for_simulator() (cleosim.InterfaceDevice method) (cleosim.Stimulator method) (cleosim.visualization.VideoVisualizer method) init_opto_syn_vars() (cleosim.opto.FourStateModel method) (cleosim.opto.OpsinModel method) inject_device() (cleosim.CLSimulator method) inject_recorder() (cleosim.CLSimulator method) inject_stimulator() (cleosim.CLSimulator method) InterfaceDevice (class in cleosim) io_processor (cleosim.CLSimulator attribute) IOProcessor (class in cleosim) is_sampling_now() (cleosim.IOProcessor method) (cleosim.processing.LatencyIOProcessor method) L LatencyIOProcessor (class in cleosim.processing) lfp_uV (cleosim.electrodes.TKLFPSignal attribute) linear_shank_coords() (in module cleosim.electrodes) M MarkovModel (class in cleosim.opto) max_Irr0_mW_per_mm2 (cleosim.opto.OptogeneticIntervention attribute) max_Irr0_mW_per_mm2_viz (cleosim.opto.OptogeneticIntervention attribute) model (cleosim.opto.FourStateModel attribute) (cleosim.opto.OpsinModel attribute) (cleosim.opto.ProportionalCurrentModel attribute) modify_model_and_params_for_ng() (cleosim.opto.OpsinModel method) (cleosim.opto.ProportionalCurrentModel method) modify_model_with_eqs() (in module cleosim.utilities) module cleosim cleosim.coordinates cleosim.electrodes cleosim.opto cleosim.processing cleosim.recorders cleosim.stimulators cleosim.utilities cleosim.visualization MultiUnitSpiking (class in cleosim.electrodes) N n (cleosim.electrodes.Probe attribute) name (cleosim.electrodes.Signal attribute) (cleosim.InterfaceDevice attribute) (cleosim.Recorder attribute) (cleosim.recorders.GroundTruthSpikeRecorder attribute) (cleosim.recorders.RateRecorder attribute) (cleosim.recorders.VoltageRecorder attribute) (cleosim.stimulators.StateVariableSetter attribute) (cleosim.visualization.VideoVisualizer attribute) network (cleosim.CLSimulator attribute) O OpsinModel (class in cleosim.opto) opto_syns (cleosim.opto.OptogeneticIntervention attribute) OptogeneticIntervention (class in cleosim.opto) P params (cleosim.opto.OpsinModel attribute) perfect_detection_radius (cleosim.electrodes.MultiUnitSpiking attribute) (cleosim.electrodes.SortedSpiking attribute) (cleosim.electrodes.Spiking attribute) PIController (class in cleosim.processing) plot() (in module cleosim.visualization) poly2_shank_coords() (in module cleosim.electrodes) poly3_shank_coords() (in module cleosim.electrodes) Probe (class in cleosim.electrodes) probe (cleosim.electrodes.Signal attribute) process() (cleosim.processing.LatencyIOProcessor method) (cleosim.processing.ProcessingBlock method) (cleosim.processing.RecordOnlyProcessor method) ProcessingBlock (class in cleosim.processing) ProportionalCurrentModel (class in cleosim.opto) put_state() (cleosim.IOProcessor method) (cleosim.processing.LatencyIOProcessor method) R RateRecorder (class in cleosim.recorders) Recorder (class in cleosim) recorders (cleosim.CLSimulator attribute) RecordOnlyProcessor (class in cleosim.processing) ref_signal (cleosim.processing.PIController attribute) required_vars (cleosim.opto.MarkovModel attribute) (cleosim.opto.OpsinModel attribute) reset() (cleosim.CLSimulator method) (cleosim.electrodes.Probe method) (cleosim.electrodes.Signal method) (cleosim.electrodes.Spiking method) (cleosim.electrodes.TKLFPSignal method) (cleosim.IOProcessor method) (cleosim.opto.OptogeneticIntervention method) (cleosim.Recorder method) (cleosim.Stimulator method) run() (cleosim.CLSimulator method) S sample_period_ms (cleosim.IOProcessor attribute) (cleosim.processing.RecordOnlyProcessor attribute) save_history (cleosim.electrodes.MultiUnitSpiking attribute) (cleosim.electrodes.SortedSpiking attribute) (cleosim.electrodes.Spiking attribute) (cleosim.electrodes.TKLFPSignal attribute) (cleosim.processing.FiringRateEstimator attribute) (cleosim.processing.ProcessingBlock attribute) (cleosim.Stimulator attribute) (cleosim.stimulators.StateVariableSetter attribute) set_io_processor() (cleosim.CLSimulator method) Signal (class in cleosim.electrodes) signals (cleosim.electrodes.Probe attribute) sim (cleosim.InterfaceDevice attribute) (cleosim.Recorder attribute) (cleosim.recorders.GroundTruthSpikeRecorder attribute) (cleosim.recorders.RateRecorder attribute) (cleosim.recorders.VoltageRecorder attribute) (cleosim.stimulators.StateVariableSetter attribute) (cleosim.visualization.VideoVisualizer attribute) SortedSpiking (class in cleosim.electrodes) Spiking (class in cleosim.electrodes) StateVariableSetter (class in cleosim.stimulators) Stimulator (class in cleosim) stimulators (cleosim.CLSimulator attribute) style_plots_for_docs() (in module cleosim.utilities) T t_in_ms (cleosim.processing.FiringRateEstimator attribute) (cleosim.processing.ProcessingBlock attribute) t_ms (cleosim.electrodes.MultiUnitSpiking attribute) (cleosim.electrodes.SortedSpiking attribute) (cleosim.electrodes.Spiking attribute) (cleosim.electrodes.TKLFPSignal attribute) (cleosim.Stimulator attribute) (cleosim.stimulators.StateVariableSetter attribute) t_out_ms (cleosim.processing.FiringRateEstimator attribute) (cleosim.processing.ProcessingBlock attribute) t_samp_ms (cleosim.electrodes.MultiUnitSpiking attribute) (cleosim.electrodes.SortedSpiking attribute) (cleosim.electrodes.Spiking attribute) (cleosim.processing.LatencyIOProcessor attribute) (cleosim.processing.RecordOnlyProcessor attribute) tetrode_shank_coords() (in module cleosim.electrodes) tile_coords() (in module cleosim.electrodes) TKLFPSignal (class in cleosim.electrodes) U uLFP_threshold_uV (cleosim.electrodes.TKLFPSignal attribute) uniform_cylinder_rθz() (in module cleosim.utilities) update() (cleosim.opto.OptogeneticIntervention method) (cleosim.Stimulator method) (cleosim.stimulators.StateVariableSetter method) update_artists() (cleosim.InterfaceDevice method) (cleosim.opto.OptogeneticIntervention method) update_stimulators() (cleosim.CLSimulator method) V value (cleosim.Stimulator attribute) (cleosim.stimulators.StateVariableSetter attribute) values (cleosim.processing.FiringRateEstimator attribute) (cleosim.processing.ProcessingBlock attribute) (cleosim.Stimulator attribute) (cleosim.stimulators.StateVariableSetter attribute) VideoVisualizer (class in cleosim.visualization) VoltageRecorder (class in cleosim.recorders) W wavelength_to_rgb() (in module cleosim.utilities) X xs (cleosim.electrodes.Probe property) xyz_from_rθz() (in module cleosim.utilities) Y ys (cleosim.electrodes.Probe property) Z zs (cleosim.electrodes.Probe property)