Index A | B | C | D | E | F | G | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z A A (cleo.imaging.DoubExpCalBindingActivation attribute) a (cleo.opto.BansalThreeStatePump attribute) action_spectrum (cleo.opto.Opsin property) add_self_to_plot() (cleo.ephys.Probe method) (cleo.imaging.Scope method) (cleo.InterfaceDevice method) (cleo.light.Light method) add_signals() (cleo.ephys.Probe method) add_to_neo_segment() (in module cleo.utilities) amp_func (cleo.ephys.RWSLFPSignalBase attribute) analog_signal() (in module cleo.utilities) area0 (cleo.light.GaussianEllipsoid property) (cleo.light.KoehlerBeam property) (cleo.light.LightModel property) (cleo.light.OpticFiber property) 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) assign_xyz() (in module cleo.coords) ax (cleo.viz.VideoVisualizer attribute) B b (cleo.opto.BansalThreeStatePump attribute) B_T (cleo.imaging.DynamicCalcium attribute) BansalFourStateOpsin (class in cleo.opto) BansalThreeStatePump (class in cleo.opto) bind_act_model (cleo.imaging.GECI attribute) brian_objects (cleo.ephys.LFPSignalBase attribute) (cleo.ephys.Signal attribute) (cleo.InterfaceDevice attribute) (cleo.registry.DeviceInteractionRegistry attribute) brian_safe_name() (in module cleo.utilities) C Ca_rest (cleo.imaging.DoubExpCalBindingActivation attribute) (cleo.imaging.DynamicCalcium attribute) cal_model (cleo.imaging.GECI attribute) CalBindingActivationModel (class in cleo.imaging) CalciumModel (class in cleo.imaging) chr2_4s() (in module cleo.opto) chr2_b4s() (in module cleo.opto) chr2_h134r_4s() (in module cleo.opto) chrimson_4s() (in module cleo.opto) Cl_out (cleo.opto.BansalThreeStatePump attribute) cleo module cleo.coords module cleo.ephys module cleo.imaging module cleo.ioproc module cleo.light module cleo.opto module cleo.recorders module cleo.registry module cleo.stimulators module cleo.utilities module cleo.viz module CLSimulator (class in cleo) collision_prob_fn (cleo.ephys.MultiUnitActivity attribute) (cleo.ephys.SortedSpiking attribute) (cleo.ephys.Spiking attribute) color (cleo.light.Light property) concat_coords() (in module cleo.coords) connect_light_to_ldd_for_ng() (cleo.registry.DeviceInteractionRegistry method) connect_to_neuron_group() (cleo.ephys.Probe method) (cleo.ephys.RWSLFPSignalFromPSCs method) (cleo.ephys.RWSLFPSignalFromSpikes method) (cleo.ephys.Signal method) (cleo.ephys.SortedSpiking method) (cleo.ephys.Spiking method) (cleo.ephys.TKLFPSignal method) (cleo.imaging.Scope method) (cleo.InterfaceDevice method) (cleo.light.Light method) (cleo.recorders.GroundTruthSpikeRecorder method) (cleo.recorders.RateRecorder method) (cleo.recorders.VoltageRecorder method) (cleo.stimulators.StateVariableSetter method) (cleo.SynapseDevice method) (cleo.viz.VideoVisualizer method) connections (cleo.registry.DeviceInteractionRegistry attribute) coords (cleo.ephys.Probe attribute) (cleo.light.Light attribute) coords_from_ng() (in module cleo.coords) coords_from_xyz() (in module cleo.coords) cubic_interpolator() (in module cleo.light) D dCa_T (cleo.imaging.DynamicCalcium attribute) DeviceInteractionRegistry (class in cleo.registry) devices (cleo.CLSimulator attribute) (cleo.viz.VideoVisualizer attribute) dFF (cleo.imaging.Scope attribute) dFF_1AP (cleo.imaging.Scope property) (cleo.imaging.Sensor attribute) dFF_max (cleo.imaging.GECI attribute) direction (cleo.imaging.Scope attribute) (cleo.light.Light attribute) DoubExpCalBindingActivation (class in cleo.imaging) dt (cleo.viz.VideoVisualizer attribute) DynamicCalcium (class in cleo.imaging) E E (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.BansalThreeStatePump attribute) (cleo.opto.FourStateOpsin attribute) E_Cl0 (cleo.opto.BansalThreeStatePump attribute) eap_decay_fn (cleo.ephys.Spiking attribute) enphr3_3s() (in module cleo.opto) epsilon() (cleo.light.LightDependent method) equal_photon_flux_spectrum() (in module cleo.light) exc_model (cleo.imaging.GECI attribute) exc_spectrum (cleo.imaging.Sensor property) ExcitationModel (class in cleo.imaging) exp_firing_rate_estimate() (in module cleo.ioproc) extra_namespace (cleo.SynapseDevice attribute) extrapolate (cleo.light.LightDependent attribute) F fiber473nm() (in module cleo.light) fig (cleo.viz.VideoVisualizer attribute) fluor_model (cleo.imaging.GECI attribute) focus_coords (cleo.imaging.Scope property) focus_coords_per_injct (cleo.imaging.Scope attribute) focus_depth (cleo.imaging.Scope attribute) FourStateOpsin (class in cleo.opto) G g0 (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.BansalThreeStatePump attribute) (cleo.opto.FourStateOpsin attribute) g_Cl (cleo.opto.BansalThreeStatePump attribute) gamma (cleo.imaging.DynamicCalcium attribute) (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) GaussianEllipsoid (class in cleo.light) Gb0 (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) gcamp3() (in module cleo.imaging) gcamp6_rs06() (in module cleo.imaging) gcamp6_rs09() (in module cleo.imaging) gcamp6f() (in module cleo.imaging) gcamp6s() (in module cleo.imaging) Gd (cleo.opto.BansalThreeStatePump attribute) Gd1 (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) Gd2 (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) GECI (class in cleo.imaging) geci() (in module cleo.imaging) generate_Animation() (cleo.viz.VideoVisualizer method) get_ctrl_signals() (cleo.ioproc.LatencyIOProcessor method) (cleo.IOProcessor method) (cleo.LatencyIOProcessor method) get_orth_vectors_for_V() (in module cleo.utilities) get_state() (cleo.CLSimulator method) (cleo.ephys.MultiUnitActivity method) (cleo.ephys.Probe method) (cleo.ephys.RWSLFPSignalBase method) (cleo.ephys.Signal method) (cleo.ephys.SortedSpiking method) (cleo.ephys.Spiking method) (cleo.ephys.TKLFPSignal method) (cleo.imaging.GECI method) (cleo.imaging.Scope method) (cleo.imaging.Sensor method) (cleo.Recorder method) (cleo.recorders.GroundTruthSpikeRecorder method) (cleo.recorders.RateRecorder method) (cleo.recorders.VoltageRecorder method) get_stim_values() (cleo.IOProcessor method) Gf0 (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) Gr (cleo.opto.BansalThreeStatePump 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_ng_by_i_probe (cleo.ephys.Spiking attribute) i_ng_by_i_sorted (cleo.ephys.SortedSpiking property) I_per_Irr (cleo.opto.ProportionalCurrentOpsin attribute) i_probe_by_ng (cleo.ephys.Spiking attribute) i_sorted_by_ng() (cleo.ephys.SortedSpiking method) i_targets_for_neuron_group() (cleo.imaging.Scope method) i_targets_per_injct (cleo.imaging.Scope attribute) I_threshold (cleo.ephys.RWSLFPSignalFromSpikes attribute) img_width (cleo.imaging.Scope attribute) init_for_probe() (cleo.ephys.Signal method) init_for_simulator() (cleo.InterfaceDevice method) (cleo.light.Light method) (cleo.viz.VideoVisualizer method) init_register_light() (cleo.registry.DeviceInteractionRegistry method) init_syn_vars() (cleo.imaging.DoubExpCalBindingActivation method) (cleo.imaging.DynamicCalcium method) (cleo.imaging.GECI method) (cleo.opto.BansalFourStateOpsin method) (cleo.opto.BansalThreeStatePump method) (cleo.opto.FourStateOpsin method) (cleo.SynapseDevice method) inject() (cleo.CLSimulator method) inject_sensor_for_targets() (cleo.imaging.Scope method) InterfaceDevice (class in cleo) io_processor (cleo.CLSimulator attribute) IOProcessor (class in cleo) irradiance (cleo.light.Light property) irradiance_ (cleo.light.Light property) is_sampling_now() (cleo.ioproc.LatencyIOProcessor method) (cleo.IOProcessor method) (cleo.LatencyIOProcessor method) J jgcamp7b() (in module cleo.imaging) jgcamp7c() (in module cleo.imaging) jgcamp7f() (in module cleo.imaging) jgcamp7s() (in module cleo.imaging) K K (cleo.light.OpticFiber attribute) k1 (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) k2 (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) K_d (cleo.imaging.GECI attribute) ka (cleo.opto.BansalThreeStatePump attribute) kappa_S (cleo.imaging.DynamicCalcium attribute) kb (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) kd (cleo.opto.BansalThreeStatePump attribute) kf (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) KoehlerBeam (class in cleo.light) L LatencyIOProcessor (class in cleo) (class in cleo.ioproc) latest_ctrl_signal (cleo.IOProcessor attribute) ldds_for_ng (cleo.registry.DeviceInteractionRegistry attribute) lfp (cleo.ephys.LFPSignalBase attribute) LFPSignalBase (class in cleo.ephys) Light (class in cleo.light) light_agg_ngs (cleo.light.LightDependent property) light_model (cleo.light.Light attribute) light_prop_model (cleo.registry.DeviceInteractionRegistry attribute) light_prop_syns (cleo.registry.DeviceInteractionRegistry attribute) light_source_ng (cleo.registry.DeviceInteractionRegistry attribute) LightDependent (class in cleo.light) LightExcitation (class in cleo.imaging) LightModel (class in cleo.light) lights_for_ng (cleo.registry.DeviceInteractionRegistry attribute) linear_interpolator() (in module cleo.light) linear_shank_coords() (in module cleo.ephys) location (cleo.imaging.GECI attribute) (cleo.imaging.Scope attribute) (cleo.imaging.Sensor attribute) log_linear_interpolator() (in module cleo.light) log_makima_interpolator() (in module cleo.light) log_pchip_interpolator() (in module cleo.light) M makima_interpolator() (in module cleo.light) max_value (cleo.light.Light attribute) max_value_viz (cleo.light.Light attribute) model (cleo.imaging.CalBindingActivationModel attribute) (cleo.imaging.CalciumModel attribute) (cleo.imaging.DoubExpCalBindingActivation attribute) (cleo.imaging.DynamicCalcium attribute) (cleo.imaging.ExcitationModel attribute) (cleo.imaging.LightExcitation attribute) (cleo.imaging.NullBindingActivation attribute) (cleo.imaging.NullExcitation attribute) (cleo.imaging.PreexistingCalcium attribute) (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.BansalThreeStatePump attribute) (cleo.opto.FourStateOpsin attribute) (cleo.opto.ProportionalCurrentOpsin attribute) (cleo.SynapseDevice attribute) modify_model_and_params_for_ng() (cleo.SynapseDevice method) modify_model_with_eqs() (in module cleo.utilities) module cleo cleo.coords cleo.ephys cleo.imaging cleo.ioproc cleo.light cleo.opto cleo.recorders cleo.registry cleo.stimulators cleo.utilities cleo.viz mon (cleo.recorders.RateRecorder attribute) (cleo.recorders.VoltageRecorder attribute) MultiUnitActivity (class in cleo.ephys) N n (cleo.ephys.MultiUnitActivity property) (cleo.ephys.Probe property) (cleo.ephys.SortedSpiking property) (cleo.ephys.Spiking property) (cleo.imaging.Scope property) (cleo.light.Light property) n_channels (cleo.ephys.Spiking property) n_H (cleo.imaging.GECI attribute) n_neurons (cleo.ephys.Spiking property) n_sorted (cleo.ephys.SortedSpiking property) NAfib (cleo.light.OpticFiber attribute) name (cleo.ephys.LFPSignalBase attribute) (cleo.ephys.Signal attribute) (cleo.InterfaceDevice attribute) NeoExportable (class in cleo) network (cleo.CLSimulator attribute) neuron_group (cleo.recorders.GroundTruthSpikeRecorder attribute) neuron_groups (cleo.imaging.Scope attribute) (cleo.stimulators.StateVariableSetter attribute) (cleo.viz.VideoVisualizer attribute) normalize_coords() (in module cleo.utilities) ntis (cleo.light.OpticFiber attribute) NullBindingActivation (class in cleo.imaging) NullExcitation (class in cleo.imaging) O ogb_1() (in module cleo.imaging) on_pre (cleo.imaging.CalciumModel attribute) (cleo.imaging.DynamicCalcium attribute) (cleo.SynapseDevice attribute) Opsin (class in cleo.opto) OpticFiber (class in cleo.light) out_buffer (cleo.ioproc.LatencyIOProcessor attribute) (cleo.ioproc.RecordOnlyProcessor attribute) (cleo.LatencyIOProcessor attribute) P p (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.BansalThreeStatePump attribute) (cleo.opto.FourStateOpsin attribute) params (cleo.imaging.GECI property) (cleo.SynapseDevice property) pchip_interpolator() (in module cleo.light) per_ng_unit_replacements (cleo.SynapseDevice attribute) phim (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.BansalThreeStatePump attribute) (cleo.opto.FourStateOpsin attribute) pi_ctrl() (in module cleo.ioproc) plot() (in module cleo.viz) plot_spectra() (in module cleo.light) poly2_shank_coords() (in module cleo.ephys) poly3_shank_coords() (in module cleo.ephys) pop_aggregate (cleo.ephys.RWSLFPSignalBase attribute) power (cleo.light.Light property) power_ (cleo.light.Light property) PreexistingCalcium (class in cleo.imaging) preprocess_ctrl_signals() (cleo.IOProcessor method) Probe (class in cleo.ephys) probe (cleo.ephys.LFPSignalBase attribute) (cleo.ephys.Signal attribute) process() (cleo.ioproc.LatencyIOProcessor method) (cleo.ioproc.RecordOnlyProcessor method) (cleo.LatencyIOProcessor method) processing (cleo.ioproc.LatencyIOProcessor attribute) (cleo.ioproc.RecordOnlyProcessor attribute) (cleo.LatencyIOProcessor attribute) ProportionalCurrentOpsin (class in cleo.opto) Psi0 (cleo.opto.BansalThreeStatePump attribute) put_state() (cleo.ioproc.LatencyIOProcessor method) (cleo.IOProcessor method) (cleo.LatencyIOProcessor method) Q q (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.BansalThreeStatePump attribute) (cleo.opto.FourStateOpsin attribute) R r0 (cleo.ephys.Spiking attribute) R0 (cleo.light.OpticFiber attribute) r_cutoff (cleo.ephys.SortedSpiking property) r_for_recall() (cleo.ephys.Spiking method) r_for_snr() (cleo.ephys.Spiking method) r_noise_floor (cleo.ephys.Spiking attribute) r_threshold (cleo.ephys.Spiking property) radius (cleo.light.KoehlerBeam attribute) RateRecorder (class in cleo.recorders) recall_by_distance() (cleo.ephys.Spiking method) recall_by_snr() (cleo.ephys.Spiking method) Recorder (class in cleo) recorders (cleo.CLSimulator attribute) recording_recall_cutoff (cleo.ephys.Spiking attribute) RecordOnlyProcessor (class in cleo.ioproc) register() (cleo.registry.DeviceInteractionRegistry method) register_ldd() (cleo.registry.DeviceInteractionRegistry method) register_light() (cleo.registry.DeviceInteractionRegistry method) registry (cleo.CLSimulator attribute) required_vars (cleo.opto.ProportionalCurrentOpsin attribute) (cleo.SynapseDevice attribute) reset() (cleo.CLSimulator method) (cleo.ephys.Probe method) (cleo.ephys.RWSLFPSignalBase method) (cleo.ephys.RWSLFPSignalFromPSCs method) (cleo.ephys.Signal method) (cleo.ephys.Spiking method) (cleo.ephys.TKLFPSignal method) (cleo.imaging.Scope method) (cleo.InterfaceDevice method) (cleo.IOProcessor method) (cleo.Stimulator method) (cleo.SynapseDevice method) rho_rel_per_injct (cleo.imaging.Scope attribute) rng (in module cleo.utilities) run() (cleo.CLSimulator method) RWSLFPSignalBase (class in cleo.ephys) RWSLFPSignalFromPSCs (class in cleo.ephys) RWSLFPSignalFromSpikes (class in cleo.ephys) S S (cleo.light.OpticFiber attribute) sample_period (cleo.IOProcessor attribute) sampling (cleo.ioproc.LatencyIOProcessor attribute) (cleo.ioproc.RecordOnlyProcessor attribute) (cleo.LatencyIOProcessor attribute) save_history (cleo.InterfaceDevice attribute) Scope (class in cleo.imaging) Sensor (class in cleo.imaging) sensor (cleo.imaging.Scope attribute) set_io_processor() (cleo.CLSimulator method) set_seed() (in module cleo.utilities) sigma_axial (cleo.light.GaussianEllipsoid attribute) sigma_lateral (cleo.light.GaussianEllipsoid attribute) sigma_noise (cleo.imaging.Scope property) (cleo.imaging.Sensor attribute) sigma_per_injct (cleo.imaging.Scope attribute) Signal (class in cleo.ephys) signals (cleo.ephys.Probe attribute) sim (cleo.InterfaceDevice attribute) (cleo.registry.DeviceInteractionRegistry attribute) simulate_false_positives (cleo.ephys.Spiking attribute) snr (cleo.imaging.Sensor property) snr_by_distance() (cleo.ephys.Spiking method) snr_cutoff (cleo.ephys.SortedSpiking attribute) (cleo.imaging.Scope attribute) soma_radius (cleo.imaging.Scope attribute) sorted_units_snr (cleo.ephys.SortedSpiking property) SortedSpiking (class in cleo.ephys) source (cleo.light.Light property) source_for_light() (cleo.registry.DeviceInteractionRegistry method) source_ngs (cleo.SynapseDevice attribute) spectrum (cleo.light.LightDependent attribute) spectrum_interpolator (cleo.light.LightDependent attribute) spike_amplitude_cv (cleo.ephys.Spiking attribute) 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) style_plots_for_paper() (in module cleo.utilities) subgroup_idx_for_light (cleo.registry.DeviceInteractionRegistry attribute) syn_delay (cleo.ephys.RWSLFPSignalFromSpikes attribute) SynapseDevice (class in cleo) synapses (cleo.SynapseDevice attribute) T t (cleo.ephys.LFPSignalBase attribute) (cleo.ephys.Spiking attribute) (cleo.imaging.Scope attribute) (cleo.Stimulator attribute) t_samp (cleo.ephys.Spiking attribute) (cleo.ioproc.LatencyIOProcessor attribute) (cleo.ioproc.RecordOnlyProcessor attribute) (cleo.LatencyIOProcessor attribute) target_neurons_in_plane() (cleo.imaging.Scope method) (in module cleo.imaging) tau1_ampa (cleo.ephys.RWSLFPSignalFromSpikes attribute) tau1_gaba (cleo.ephys.RWSLFPSignalFromSpikes attribute) tau2_ampa (cleo.ephys.RWSLFPSignalFromSpikes attribute) tau2_gaba (cleo.ephys.RWSLFPSignalFromSpikes attribute) tau_off (cleo.imaging.DoubExpCalBindingActivation attribute) tau_on (cleo.imaging.DoubExpCalBindingActivation attribute) tetrode_shank_coords() (in module cleo.ephys) threshold_sigma (cleo.ephys.Spiking attribute) 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.LFPSignalBase method) (cleo.ephys.MultiUnitActivity method) (cleo.ephys.Probe method) (cleo.ephys.RWSLFPSignalBase method) (cleo.ephys.Spiking method) (cleo.imaging.Scope method) (cleo.light.Light method) (cleo.NeoExportable method) (cleo.Stimulator method) tp_light_from_scope() (in module cleo.light) transmittance() (cleo.light.GaussianEllipsoid method) (cleo.light.KoehlerBeam method) (cleo.light.Light method) (cleo.light.LightModel method) (cleo.light.OpticFiber method) U uLFP_threshold (cleo.ephys.TKLFPSignal attribute) uniform_cylinder_rθz() (in module cleo.utilities) unit (cleo.stimulators.StateVariableSetter attribute) unit_safe_allclose() (in module cleo.utilities) unit_safe_append() (in module cleo.utilities) unit_safe_cat() (in module cleo.utilities) unit_safe_round() (in module cleo.utilities) update() (cleo.light.Light method) (cleo.Stimulator method) (cleo.stimulators.StateVariableSetter method) update_artists() (cleo.InterfaceDevice method) (cleo.light.Light method) update_stimulators() (cleo.CLSimulator method) V v0 (cleo.opto.FourStateOpsin attribute) v1 (cleo.opto.FourStateOpsin attribute) value (cleo.Stimulator attribute) values (cleo.Stimulator attribute) variable_to_ctrl (cleo.stimulators.StateVariableSetter attribute) vartheta_max (cleo.opto.BansalThreeStatePump attribute) vfchrimson_4s() (in module cleo.opto) VideoVisualizer (class in cleo.viz) viz_params() (cleo.light.GaussianEllipsoid method) (cleo.light.KoehlerBeam method) (cleo.light.LightModel method) (cleo.light.OpticFiber method) vmax (cleo.opto.BansalThreeStatePump attribute) vmin (cleo.opto.BansalThreeStatePump attribute) voltage_var_name (cleo.recorders.VoltageRecorder attribute) VoltageRecorder (class in cleo.recorders) W wavelength (cleo.light.Light attribute) wavelength_to_rgb() (in module cleo.utilities) weight (cleo.ephys.RWSLFPSignalFromSpikes attribute) wslfp_kwargs (cleo.ephys.RWSLFPSignalBase attribute) X xs (cleo.ephys.Probe property) xyz_from_rθz() (in module cleo.utilities) Y ys (cleo.ephys.Probe property) Z zmax (cleo.light.KoehlerBeam attribute) zs (cleo.ephys.Probe property)