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