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) 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) 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) assign_xyz() (in module cleo.coords) ax (cleo.viz.VideoVisualizer attribute) B B_T (cleo.imaging.DynamicCalcium attribute) BansalFourStateOpsin (class in cleo.opto) bind_act_model (cleo.imaging.GECI attribute) brian_objects (cleo.ephys.Signal attribute) (cleo.InterfaceDevice attribute) 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) chrimson_4s() (in module cleo.opto) 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) 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.coords) connect_light_to_ldd_for_ng() (cleo.registry.DeviceInteractionRegistry 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.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) ConstantDelay (class in cleo.ioproc) 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) cutoff_probability (cleo.ephys.Spiking attribute) D dCa_T (cleo.imaging.DynamicCalcium attribute) default_value (cleo.light.Light attribute) (cleo.Stimulator attribute) Delay (class in cleo.ioproc) delay (cleo.ioproc.FiringRateEstimator attribute) (cleo.ioproc.ProcessingBlock 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.FourStateOpsin attribute) 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) extra_namespace (cleo.opto.FourStateOpsin attribute) (cleo.SynapseDevice attribute) F fiber473nm() (in module cleo.light) fig (cleo.viz.VideoVisualizer attribute) FiringRateEstimator (class in cleo.ioproc) fluor_model (cleo.imaging.GECI attribute) 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.FourStateOpsin attribute) gamma (cleo.imaging.DynamicCalcium attribute) (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) GaussianDelay (class in cleo.ioproc) GaussianEllipsoid (class in cleo.light) Gb0 (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) gcamp3() (in module cleo.imaging) gcamp6f() (in module cleo.imaging) gcamp6rs06() (in module cleo.imaging) gcamp6rs09() (in module cleo.imaging) gcamp6s() (in module cleo.imaging) 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_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.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) 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) i_targets_for_neuron_group() (cleo.imaging.Scope method) i_targets_per_injct (cleo.imaging.Scope attribute) img_width (cleo.imaging.Scope attribute) init_for_probe() (cleo.ephys.Signal method) (cleo.ephys.TKLFPSignal 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.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) is_sampling_now() (cleo.ioproc.LatencyIOProcessor method) (cleo.IOProcessor 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) kappa_S (cleo.imaging.DynamicCalcium 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) ldds_for_ng (cleo.registry.DeviceInteractionRegistry attribute) lfp_uV (cleo.ephys.TKLFPSignal attribute) 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) M max_Irr0_mW_per_mm2 (cleo.light.Light attribute) max_Irr0_mW_per_mm2_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.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) MultiUnitSpiking (class in cleo.ephys) N n (cleo.ephys.Probe property) (cleo.imaging.Scope property) (cleo.light.Light property) n_H (cleo.imaging.GECI attribute) NAfib (cleo.light.OpticFiber attribute) name (cleo.ephys.Signal attribute) (cleo.InterfaceDevice attribute) 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 ogb1() (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) P p (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) params (cleo.imaging.GECI property) (cleo.SynapseDevice property) per_ng_unit_replacements (cleo.SynapseDevice attribute) phim (cleo.opto.BansalFourStateOpsin attribute) (cleo.opto.FourStateOpsin attribute) PIController (class in 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) PreexistingCalcium (class in cleo.imaging) 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.light.OpticFiber attribute) r_half_detection (cleo.ephys.Spiking attribute) r_perfect_detection (cleo.ephys.Spiking attribute) rand_seed (cleo.imaging.Scope 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() (cleo.registry.DeviceInteractionRegistry method) register_ldd() (cleo.registry.DeviceInteractionRegistry method) register_light() (cleo.registry.DeviceInteractionRegistry method) registries (in module cleo.registry) registry_for_sim() (in module cleo.registry) required_vars (cleo.opto.ProportionalCurrentOpsin attribute) (cleo.SynapseDevice attribute) reset() (cleo.CLSimulator method) (cleo.ephys.Probe 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) S S (cleo.light.OpticFiber attribute) sample_period_ms (cleo.ioproc.RecordOnlyProcessor attribute) (cleo.IOProcessor attribute) save_history (cleo.InterfaceDevice attribute) (cleo.ioproc.FiringRateEstimator attribute) (cleo.ioproc.ProcessingBlock attribute) Scope (class in cleo.imaging) Sensor (class in cleo.imaging) sensor (cleo.imaging.Scope attribute) set_io_processor() (cleo.CLSimulator method) 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) snr (cleo.imaging.Sensor property) snr_cutoff (cleo.imaging.Scope attribute) soma_radius (cleo.imaging.Scope attribute) 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) (cleo.opto.Opsin attribute) spectrum_interpolator (cleo.light.LightDependent attribute) (cleo.opto.Opsin 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) subgroup_idx_for_light (cleo.registry.DeviceInteractionRegistry attribute) SynapseDevice (class in cleo) synapses (cleo.SynapseDevice attribute) T t_in_ms (cleo.ioproc.FiringRateEstimator attribute) (cleo.ioproc.ProcessingBlock attribute) t_ms (cleo.ephys.Spiking attribute) (cleo.ephys.TKLFPSignal attribute) (cleo.imaging.Scope 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) target_neurons_in_plane() (cleo.imaging.Scope method) (in module cleo.imaging) tau_off (cleo.imaging.DoubExpCalBindingActivation attribute) tau_on (cleo.imaging.DoubExpCalBindingActivation 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.light.Light method) (cleo.Stimulator method) tp_light_from_scope() (in module cleo.light) transmittance() (cleo.light.GaussianEllipsoid method) (cleo.light.Light method) (cleo.light.LightModel method) (cleo.light.OpticFiber method) U uLFP_threshold_uV (cleo.ephys.TKLFPSignal attribute) uniform_cylinder_rθz() (in module cleo.utilities) unit (cleo.stimulators.StateVariableSetter attribute) 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.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_params() (cleo.light.GaussianEllipsoid method) (cleo.light.LightModel method) (cleo.light.OpticFiber method) 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) 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)