Index A | B | C | D | E | F | G | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z A action_spectrum (cleo.opto.Opsin attribute) action_spectrum_interpolator (cleo.opto.Opsin attribute) add_self_to_plot() (cleo.ephys.Probe method) (cleo.InterfaceDevice method) (cleo.opto.Light method) add_signals() (cleo.ephys.Probe method) add_to_neo_segment() (in module cleo.utilities) analog_signal() (in module cleo.utilities) 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) ax (cleo.viz.VideoVisualizer attribute) B BansalFourStateOpsin (class in cleo.opto) brian_objects (cleo.ephys.Signal attribute) (cleo.InterfaceDevice attribute) C chr2_4s() (in module cleo.opto) chr2_b4s() (in module cleo.opto) chrimson_4s() (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_light_to_opsin_for_ng() (cleo.opto.LightOpsinRegistry method) 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.Light method) (cleo.opto.Opsin method) (cleo.recorders.GroundTruthSpikeRecorder method) (cleo.recorders.RateRecorder method) (cleo.recorders.VoltageRecorder method) (cleo.stimulators.StateVariableSetter method) (cleo.viz.VideoVisualizer method) connections (cleo.opto.LightOpsinRegistry attribute) ConstantDelay (class in cleo.ioproc) coords (cleo.ephys.Probe attribute) (cleo.opto.Light attribute) coords_from_ng() (in module cleo.coords) coords_from_xyz() (in module cleo.coords) cubic_interpolator() (in module cleo.opto) cutoff_probability (cleo.ephys.Spiking attribute) D default_value (cleo.opto.Light attribute) (cleo.Stimulator attribute) Delay (class in cleo.ioproc) delay (cleo.ioproc.FiringRateEstimator attribute) (cleo.ioproc.ProcessingBlock attribute) devices (cleo.CLSimulator attribute) (cleo.viz.VideoVisualizer attribute) direction (cleo.opto.Light attribute) dt (cleo.viz.VideoVisualizer attribute) E E (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) epsilon() (cleo.opto.Opsin method) extra_namespace (cleo.opto.FourStateOpsin attribute) (cleo.opto.Opsin attribute) F fiber473nm() (in module cleo.opto) FiberModel (class in cleo.opto) fig (cleo.viz.VideoVisualizer attribute) FiringRateEstimator (class in cleo.ioproc) FourStateOpsin (class in cleo.opto) G g0 (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) gamma (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) GaussianDelay (class in cleo.ioproc) Gb0 (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) Gd1 (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) Gd2 (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) 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) Gf0 (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) Gr0 (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) GroundTruthSpikeRecorder (class in cleo.recorders) gtacr2_4s() (in module cleo.opto) I i (cleo.ephys.Spiking attribute) (cleo.recorders.RateRecorder attribute) I_per_Irr (cleo.opto.ProportionalCurrentOpsin attribute) i_probe_by_i_ng (cleo.ephys.Spiking attribute) init_for_probe() (cleo.ephys.Signal method) (cleo.ephys.TKLFPSignal method) init_for_simulator() (cleo.InterfaceDevice method) (cleo.opto.Light method) (cleo.viz.VideoVisualizer method) init_opto_syn_vars() (cleo.opto.BansalFourStateOpsin method) (cleo.opto.FourStateOpsin method) (cleo.opto.Opsin method) init_register_light() (cleo.opto.LightOpsinRegistry method) inject() (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) K K (cleo.opto.FiberModel attribute) k1 (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) k2 (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) kb (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) kf (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) L LatencyIOProcessor (class in cleo.ioproc) lfp_uV (cleo.ephys.TKLFPSignal attribute) Light (class in cleo.opto) light_agg_ngs (cleo.opto.Opsin attribute) light_model (cleo.opto.Light attribute) light_prop_model (cleo.opto.LightOpsinRegistry attribute) light_prop_syns (cleo.opto.LightOpsinRegistry attribute) light_source_ng (cleo.opto.LightOpsinRegistry attribute) LightModel (class in cleo.opto) LightOpsinRegistry (class in cleo.opto) lights_for_ng (cleo.opto.LightOpsinRegistry attribute) linear_interpolator() (in module cleo.opto) linear_shank_coords() (in module cleo.ephys) lor_for_sim() (in module cleo.opto) M max_Irr0_mW_per_mm2 (cleo.opto.Light attribute) max_Irr0_mW_per_mm2_viz (cleo.opto.Light attribute) model (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FiberModel attribute) (cleo.opto.FourStateOpsin attribute) (cleo.opto.Opsin attribute) (cleo.opto.ProportionalCurrentOpsin attribute) modify_model_and_params_for_ng() (cleo.opto.Opsin 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 mon (cleo.recorders.RateRecorder attribute) (cleo.recorders.VoltageRecorder attribute) MultiUnitSpiking (class in cleo.ephys) N n (cleo.ephys.Probe property) (cleo.opto.Light property) NAfib (cleo.opto.FiberModel attribute) name (cleo.ephys.Signal attribute) (cleo.InterfaceDevice attribute) network (cleo.CLSimulator attribute) neuron_group (cleo.recorders.GroundTruthSpikeRecorder attribute) neuron_groups (cleo.stimulators.StateVariableSetter attribute) (cleo.viz.VideoVisualizer attribute) normalize_coords() (in module cleo.utilities) ntis (cleo.opto.FiberModel attribute) O Opsin (class in cleo.opto) opsins_for_ng (cleo.opto.LightOpsinRegistry attribute) opto_syns (cleo.opto.Opsin attribute) P p (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) params (cleo.opto.Opsin property) per_ng_unit_replacements (cleo.opto.Opsin attribute) phim (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) PIController (class in cleo.ioproc) plot() (in module cleo.viz) plot_action_spectra() (in module cleo.opto) poly2_shank_coords() (in module cleo.ephys) poly3_shank_coords() (in module cleo.ephys) Probe (class in cleo.ephys) probe (cleo.ephys.Probe attribute) (cleo.ephys.Signal attribute) process() (cleo.ioproc.LatencyIOProcessor method) (cleo.ioproc.ProcessingBlock method) (cleo.ioproc.RecordOnlyProcessor method) ProcessingBlock (class in cleo.ioproc) ProportionalCurrentOpsin (class in cleo.opto) put_state() (cleo.ioproc.LatencyIOProcessor method) (cleo.IOProcessor method) Q q (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) R R0 (cleo.opto.FiberModel attribute) r_half_detection (cleo.ephys.Spiking attribute) r_perfect_detection (cleo.ephys.Spiking attribute) RateRecorder (class in cleo.recorders) Recorder (class in cleo) recorders (cleo.CLSimulator attribute) RecordOnlyProcessor (class in cleo.ioproc) ref_signal (cleo.ioproc.PIController attribute) register_light() (cleo.opto.LightOpsinRegistry method) register_opsin() (cleo.opto.LightOpsinRegistry method) required_vars (cleo.opto.Opsin attribute) (cleo.opto.ProportionalCurrentOpsin attribute) reset() (cleo.CLSimulator method) (cleo.ephys.Probe method) (cleo.ephys.Signal method) (cleo.ephys.Spiking method) (cleo.ephys.TKLFPSignal method) (cleo.InterfaceDevice method) (cleo.IOProcessor method) (cleo.opto.Opsin method) (cleo.Stimulator method) run() (cleo.CLSimulator method) S S (cleo.opto.FiberModel attribute) sample_period_ms (cleo.ioproc.RecordOnlyProcessor attribute) (cleo.IOProcessor attribute) save_history (cleo.ephys.Spiking attribute) (cleo.ephys.TKLFPSignal attribute) (cleo.ioproc.FiringRateEstimator attribute) (cleo.ioproc.ProcessingBlock attribute) (cleo.Stimulator attribute) set_io_processor() (cleo.CLSimulator method) Signal (class in cleo.ephys) signals (cleo.ephys.Probe attribute) sim (cleo.InterfaceDevice attribute) (cleo.opto.LightOpsinRegistry attribute) SortedSpiking (class in cleo.ephys) source (cleo.opto.Light property) source_for_light() (cleo.opto.LightOpsinRegistry method) 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) subgroup_idx_for_light (cleo.opto.LightOpsinRegistry attribute) T t_in_ms (cleo.ioproc.FiringRateEstimator attribute) (cleo.ioproc.ProcessingBlock attribute) t_ms (cleo.ephys.Spiking attribute) (cleo.ephys.TKLFPSignal attribute) (cleo.Stimulator attribute) t_out_ms (cleo.ioproc.FiringRateEstimator attribute) (cleo.ioproc.ProcessingBlock attribute) t_samp_ms (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) times_are_regular() (in module cleo.utilities) TKLFPSignal (class in cleo.ephys) to_neo() (cleo.CLSimulator method) (cleo.ephys.MultiUnitSpiking method) (cleo.ephys.Probe method) (cleo.ephys.Spiking method) (cleo.ephys.TKLFPSignal method) (cleo.opto.Light method) (cleo.Stimulator method) transmittance() (cleo.opto.FiberModel method) (cleo.opto.Light method) (cleo.opto.LightModel method) U uLFP_threshold_uV (cleo.ephys.TKLFPSignal attribute) uniform_cylinder_rθz() (in module cleo.utilities) unit (cleo.stimulators.StateVariableSetter attribute) update() (cleo.opto.Light method) (cleo.Stimulator method) (cleo.stimulators.StateVariableSetter method) update_artists() (cleo.InterfaceDevice method) (cleo.opto.Light method) update_stimulators() (cleo.CLSimulator method) V v0 (cleo.opto.FourStateOpsin attribute) v1 (cleo.opto.FourStateOpsin attribute) value (cleo.Stimulator attribute) values (cleo.ioproc.FiringRateEstimator attribute) (cleo.ioproc.ProcessingBlock attribute) (cleo.Stimulator attribute) variable_to_ctrl (cleo.stimulators.StateVariableSetter attribute) vfchrimson_4s() (in module cleo.opto) VideoVisualizer (class in cleo.viz) viz_points() (cleo.opto.FiberModel method) (cleo.opto.LightModel method) voltage_var_name (cleo.recorders.VoltageRecorder attribute) VoltageRecorder (class in cleo.recorders) W wavelength (cleo.opto.FiberModel attribute) (cleo.opto.LightModel attribute) 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)