Index Symbols | A | B | C | D | E | F | G | H | I | L | M | N | O | P | Q | R | S | T | U | V | W | Y Symbols --all-spike-hist plot-network-clamp command line option --alpha-radius generate-soma-coordinates command line option measure-distances command line option --arena-id cut-slice command line option generate-input-features command line option generate-input-spike-trains command line option run-network command line option sample-cells command line option --bgcolor plot-biophys-cell-tree command line option --cache-size generate-distance-connections command line option generate-input-features command line option generate-input-spike-trains command line option measure-distances command line option --cell-attr-gen-cache-size run-network command line option --cell-selection-path run-network command line option --checkpoint-clear-data run-network command line option --checkpoint-interval run-network command line option --chunk-size distribute-synapse-locs command line option generate-distance-connections command line option generate-input-features command line option generate-input-spike-trains command line option generate-soma-coordinates command line option measure-distances command line option --cleanup run-network command line option --color-edge-scalars plot-cell-tree command line option --colormap plot-biophys-cell-tree command line option plot-state command line option --config check-config command line option cut-slice command line option distribute-synapse-locs command line option generate-distance-connections command line option generate-input-features command line option generate-input-spike-trains command line option generate-soma-coordinates command line option make-h5types command line option measure-distances command line option plot-biophys-cell-tree command line option plot-coords-in-volume command line option sample-cells command line option --config-file plot-network-clamp command line option run-network command line option --config-prefix check-config command line option cut-slice command line option distribute-synapse-locs command line option generate-distance-connections command line option generate-input-features command line option generate-input-spike-trains command line option generate-soma-coordinates command line option make-h5types command line option measure-distances command line option plot-biophys-cell-tree command line option plot-network-clamp command line option run-network command line option sample-cells command line option --conn-loc plot-cell-tree command line option --connectivity-namespace generate-distance-connections command line option --connectivity-path generate-distance-connections command line option --coords-namespace generate-distance-connections command line option measure-distances command line option plot-coords-in-volume command line option --coords-path generate-distance-connections command line option generate-input-features command line option generate-input-spike-trains command line option measure-distances command line option plot-coords-in-volume command line option --data-file plot-biophys-cell-tree command line option --dataset-prefix cut-slice command line option plot-biophys-cell-tree command line option run-network command line option sample-cells command line option --debug distribute-synapse-locs command line option generate-distance-connections command line option generate-input-features command line option generate-input-spike-trains command line option run-network command line option --debug-count generate-input-features command line option --dispersion-delta generate-soma-coordinates command line option --distance plot-state command line option --distance-limits cut-slice command line option --distances-namespace cut-slice command line option generate-distance-connections command line option generate-input-features command line option generate-input-spike-trains command line option sample-cells command line option --distribution distribute-synapse-locs command line option --dry-run distribute-synapse-locs command line option generate-distance-connections command line option generate-input-features command line option generate-input-spike-trains command line option run-network command line option --dt run-network command line option --exclude-artificial plot-network-clamp command line option plot-spike-raster command line option --fig-format generate-input-features command line option generate-input-spike-trains command line option --fig-size plot-spike-raster command line option --font-size generate-input-features command line option generate-input-spike-trains command line option plot-biophys-cell-tree command line option plot-network-clamp command line option plot-spike-raster command line option plot-state command line option --forest-path distribute-synapse-locs command line option generate-distance-connections command line option plot-cell-tree command line option --gap-junctions make-h5types command line option --gather generate-input-features command line option generate-input-spike-trains command line option --geometry-path generate-soma-coordinates command line option measure-distances command line option --gid plot-biophys-cell-tree command line option plot-cell-tree command line option plot-network-clamp command line option plot-state command line option --hoc-lib-path run-network command line option --include generate-distance-connections command line option --include-artificial plot-network-clamp command line option plot-spike-raster command line option --input-features-namespaces sample-cells command line option --input-features-path sample-cells command line option --input-path plot-network-clamp command line option query-cell-attrs command line option show-h5types command line option --interactive generate-input-features command line option --interp-chunk-size generate-distance-connections command line option --io-size cut-slice command line option distribute-synapse-locs command line option generate-distance-connections command line option generate-input-features command line option generate-input-spike-trains command line option generate-soma-coordinates command line option measure-distances command line option run-network command line option sample-cells command line option --labels plot-network-clamp command line option plot-spike-raster command line option --ldbal run-network command line option --legend plot-network-clamp command line option --line-width plot-cell-tree command line option plot-network-clamp command line option --load-synapses plot-biophys-cell-tree command line option --lowpass-plot plot-state command line option --lowpass-plot-type plot-network-clamp command line option --lptbal run-network command line option --max-spikes plot-spike-raster command line option --max-units plot-state command line option --max-walltime-hours run-network command line option --mayavi plot-cell-tree command line option plot-coords-in-volume command line option --mechanisms-path distribute-synapse-locs command line option run-network command line option --microcircuit-inputs run-network command line option --n-trials generate-input-spike-trains command line option plot-network-clamp command line option --no-cleanup run-network command line option --no-color-edge-scalars plot-cell-tree command line option --no-conn-loc plot-cell-tree command line option --node-rank-file run-network command line option --nodeiter generate-soma-coordinates command line option --nsample measure-distances command line option --output-namespace generate-soma-coordinates command line option --output-path cut-slice command line option distribute-synapse-locs command line option generate-input-features command line option generate-input-spike-trains command line option generate-soma-coordinates command line option make-h5types command line option sample-cells command line option --output-syn-spike-count run-network command line option --phase-mod generate-input-spike-trains command line option --plot generate-input-features command line option generate-input-spike-trains command line option --plot-method plot-biophys-cell-tree command line option --population plot-biophys-cell-tree command line option plot-cell-tree command line option --populations distribute-synapse-locs command line option generate-input-features command line option generate-input-spike-trains command line option generate-soma-coordinates command line option measure-distances command line option plot-coords-in-volume command line option plot-network-clamp command line option plot-spike-raster command line option plot-state command line option query-cell-attrs command line option --profile-memory run-network command line option --query plot-state command line option --recording-profile run-network command line option --reduce plot-state command line option --resolution generate-distance-connections command line option generate-soma-coordinates command line option measure-distances command line option --results-id run-network command line option --results-path run-network command line option --results-write-time run-network command line option --save-fig generate-input-features command line option generate-input-spike-trains command line option --save-fig-dir generate-input-features command line option generate-input-spike-trains command line option --save-format plot-spike-raster command line option --scale plot-coords-in-volume command line option --selection-path sample-cells command line option --selectivity-namespace generate-input-spike-trains command line option --selectivity-path generate-input-spike-trains command line option --show-fig generate-input-features command line option generate-input-spike-trains command line option --snap-delta generate-soma-coordinates command line option --spike-events-namespace plot-spike-raster command line option --spike-events-path plot-spike-raster command line option --spike-hist-bin plot-network-clamp command line option plot-spike-raster command line option --spike-input-attr cut-slice command line option run-network command line option sample-cells command line option --spike-input-namespace cut-slice command line option run-network command line option sample-cells command line option --spike-input-path cut-slice command line option run-network command line option sample-cells command line option --spike-namespace plot-network-clamp command line option --spike-train-attr-name generate-input-spike-trains command line option --spikes-namespace generate-input-spike-trains command line option --state-namespace plot-network-clamp command line option plot-state command line option --state-namespace-pattern plot-state command line option --state-path plot-state command line option --state-variable plot-network-clamp command line option plot-state command line option --stimulus-id run-network command line option sample-cells command line option --stimulus-onset run-network command line option --subpopulation plot-coords-in-volume command line option --subvol plot-coords-in-volume command line option --syn-source-threshold plot-biophys-cell-tree command line option --syn-sources plot-biophys-cell-tree command line option --syn-types plot-biophys-cell-tree command line option --synapses-namespace generate-distance-connections command line option --t-max plot-network-clamp command line option plot-spike-raster command line option plot-state command line option --t-min plot-network-clamp command line option plot-spike-raster command line option plot-state command line option --t-variable plot-network-clamp command line option plot-spike-raster command line option plot-state command line option --target-input-features-arena-id plot-network-clamp command line option --target-input-features-namespace plot-network-clamp command line option --target-input-features-path plot-network-clamp command line option --target-input-features-trajectory-id plot-network-clamp command line option --template-path distribute-synapse-locs command line option --template-paths plot-biophys-cell-tree command line option run-network command line option --trajectory-id cut-slice command line option --tstop run-network command line option --types-path generate-soma-coordinates command line option --use-cell-attr-gen run-network command line option --use-coreneuron run-network command line option --v-init run-network command line option --value-chunk-size distribute-synapse-locs command line option generate-distance-connections command line option generate-input-features command line option generate-input-spike-trains command line option generate-soma-coordinates command line option measure-distances command line option --verbose check-config command line option cut-slice command line option distribute-synapse-locs command line option generate-distance-connections command line option generate-input-features command line option generate-input-spike-trains command line option generate-soma-coordinates command line option measure-distances command line option plot-biophys-cell-tree command line option plot-cell-tree command line option plot-coords-in-volume command line option plot-network-clamp command line option plot-spike-raster command line option plot-state command line option run-network command line option sample-cells command line option --write-selection cut-slice command line option run-network command line option --write-size distribute-synapse-locs command line option generate-distance-connections command line option generate-input-features command line option generate-input-spike-trains command line option -c cut-slice command line option make-h5types command line option plot-biophys-cell-tree command line option plot-coords-in-volume command line option sample-cells command line option -g plot-biophys-cell-tree command line option plot-cell-tree command line option plot-network-clamp command line option plot-state command line option -i distribute-synapse-locs command line option generate-distance-connections command line option generate-soma-coordinates command line option measure-distances command line option plot-cell-tree command line option plot-coords-in-volume command line option plot-network-clamp command line option plot-spike-raster command line option plot-state command line option query-cell-attrs command line option -m distribute-synapse-locs command line option plot-cell-tree command line option plot-coords-in-volume command line option run-network command line option -n cut-slice command line option generate-input-features command line option plot-coords-in-volume command line option plot-network-clamp command line option plot-spike-raster command line option plot-state command line option sample-cells command line option -o cut-slice command line option sample-cells command line option -p generate-input-features command line option generate-input-spike-trains command line option plot-biophys-cell-tree command line option plot-cell-tree command line option plot-network-clamp command line option plot-spike-raster command line option plot-state command line option query-cell-attrs command line option show-h5types command line option -q plot-state command line option -s plot-biophys-cell-tree command line option -v check-config command line option cut-slice command line option distribute-synapse-locs command line option generate-distance-connections command line option generate-input-features command line option generate-input-spike-trains command line option generate-soma-coordinates command line option measure-distances command line option plot-biophys-cell-tree command line option plot-cell-tree command line option plot-coords-in-volume command line option plot-network-clamp command line option plot-spike-raster command line option plot-state command line option run-network command line option sample-cells command line option A AbstractEnv (class in miv_simulator.utils.utils) add_mech_attrs() (miv_simulator.synapses.SynapseAttributes method) add_mech_attrs_from_iter() (miv_simulator.synapses.SynapseAttributes method) add_netcon() (miv_simulator.synapses.SynapseAttributes method) add_pps() (miv_simulator.synapses.SynapseAttributes method) add_vecstim() (miv_simulator.synapses.SynapseAttributes method) ais (miv_simulator.utils.neuron.HocCellInterface attribute) all (miv_simulator.utils.neuron.HocCellInterface attribute) alpha_shape() (in module miv_simulator.geometry.alphavol) AlphaShape (class in miv_simulator.geometry.alphavol) angular_deviation() (in module miv_simulator.geometry.alphavol) apical (miv_simulator.utils.neuron.HocCellInterface attribute) apply_mech_rules() (in module miv_simulator.cells) apply_syn_mech_rules() (in module miv_simulator.synapses) arena_rate_maps_from_features() (in module miv_simulator.stimulus) ArenaConfig (in module miv_simulator.env) axon (miv_simulator.utils.neuron.HocCellInterface attribute) B baks() (in module miv_simulator.utils.utils) basal (miv_simulator.utils.neuron.HocCellInterface attribute) bin_stimulus_features() (in module miv_simulator.stimulus) BiophysCell (class in miv_simulator.cells) bounds (miv_simulator.geometry.alphavol.AlphaShape attribute) BRKconfig (class in miv_simulator.utils.neuron) BRKneuron (class in miv_simulator.cells) C cartesian_product() (in module miv_simulator.geometry.linear_volume) (in module miv_simulator.geometry.rbf_surface) (in module miv_simulator.geometry.rbf_volume) check-config command line option --config --config-prefix --verbose -v choose_input_selectivity_type() (in module miv_simulator.stimulus) choose_synapse_projection() (in module miv_simulator.connections) circumcenters() (in module miv_simulator.geometry.alphavol) clean_axes() (in module miv_simulator.plotting) cm_ratio (miv_simulator.utils.neuron.BRKconfig attribute) (miv_simulator.utils.neuron.PRconfig attribute) compose_iter() (in module miv_simulator.utils.utils) config_biophys_cell_syns() (in module miv_simulator.synapses) config_hoc_cell_syns() (in module miv_simulator.synapses) config_syn() (in module miv_simulator.synapses) configure_hoc_env() (in module miv_simulator.utils.neuron) connect2target() (in module miv_simulator.cells) connect_cell_selection() (in module miv_simulator.network) connect_cells() (in module miv_simulator.network) connect_gjs() (in module miv_simulator.network) connect_nodes() (in module miv_simulator.cells) connection_bounds (miv_simulator.env.GapjunctionConfig attribute) connection_parameters (miv_simulator.env.GapjunctionConfig attribute) connection_probability (miv_simulator.env.GapjunctionConfig attribute) ConnectionProb (class in miv_simulator.connections) consecutive() (in module miv_simulator.utils.utils) contacts (miv_simulator.env.SynapseConfig attribute) Context (class in miv_simulator.utils.utils) contiguous_ranges() (in module miv_simulator.utils.utils) convert() (miv_simulator.utils.utils.EnumChoice method) correct_cell_for_spines_cm() (in module miv_simulator.cells) correct_cell_for_spines_g_pas() (in module miv_simulator.cells) correct_node_for_spines_cm() (in module miv_simulator.cells) correct_node_for_spines_g_pas() (in module miv_simulator.cells) coupling_bounds (miv_simulator.env.GapjunctionConfig attribute) coupling_coefficients (miv_simulator.env.GapjunctionConfig attribute) coupling_parameters (miv_simulator.env.GapjunctionConfig attribute) cut-slice command line option --arena-id --config --config-prefix --dataset-prefix --distance-limits --distances-namespace --io-size --output-path --spike-input-attr --spike-input-namespace --spike-input-path --trajectory-id --verbose --write-selection -c -n -o -v cx() (in module miv_simulator.utils.neuron) D d_lambda_nseg() (in module miv_simulator.utils.neuron) del_netcon() (miv_simulator.synapses.SynapseAttributes method) del_syn_id_attr_dict() (miv_simulator.synapses.SynapseAttributes method) dend_alpha_Caconc (miv_simulator.utils.neuron.BRKconfig attribute) dend_d_Caconc (miv_simulator.utils.neuron.PRconfig attribute) dend_f_Caconc (miv_simulator.utils.neuron.BRKconfig attribute) dend_g_pas (miv_simulator.utils.neuron.BRKconfig attribute) (miv_simulator.utils.neuron.PRconfig attribute) dend_gmax_Ca (miv_simulator.utils.neuron.PRconfig attribute) dend_gmax_CaL (miv_simulator.utils.neuron.BRKconfig attribute) dend_gmax_CaN (miv_simulator.utils.neuron.BRKconfig attribute) dend_gmax_KAHP (miv_simulator.utils.neuron.PRconfig attribute) dend_gmax_KCa (miv_simulator.utils.neuron.BRKconfig attribute) (miv_simulator.utils.neuron.PRconfig attribute) dend_kCa_Caconc (miv_simulator.utils.neuron.BRKconfig attribute) dist_ctrl() (in module miv_simulator.clamps.network) dist_run() (in module miv_simulator.clamps.network) distribute-synapse-locs command line option --chunk-size --config --config-prefix --debug --distribution --dry-run --forest-path --io-size --mechanisms-path --output-path --populations --template-path --value-chunk-size --verbose --write-size -i -m -v distribute_poisson_synapses() (in module miv_simulator.synapses) distribute_synapses() (in module miv_simulator.simulator) distribute_uniform_synapses() (in module miv_simulator.synapses) DomainConfig (in module miv_simulator.env) E e_pas (miv_simulator.utils.neuron.BRKconfig attribute) (miv_simulator.utils.neuron.PRconfig attribute) EnumChoice (class in miv_simulator.utils.utils) Env (class in miv_simulator.env) euclidean_distance() (in module miv_simulator.geometry.geometry) (in module miv_simulator.geometry.linear_volume) (in module miv_simulator.geometry.rbf_surface) (in module miv_simulator.geometry.rbf_volume) ExplicitDumper (class in miv_simulator.utils.utils) ExprClosure (class in miv_simulator.utils.utils) F feature_edges() (in module miv_simulator.geometry.alphavol) filter_by_distance() (miv_simulator.connections.ConnectionProb method) filter_nodes() (in module miv_simulator.cells) filter_synapses() (miv_simulator.synapses.SynapseAttributes method) find_gid_pop() (in module miv_simulator.network) find_template() (in module miv_simulator.utils.neuron) fit_membrane_time_constant() (in module miv_simulator.clamps.cell) free_boundary() (in module miv_simulator.geometry.alphavol) frequency (miv_simulator.stimulus.PhaseModConfig attribute) G GapjunctionConfig (class in miv_simulator.env) gc (miv_simulator.utils.neuron.BRKconfig attribute) (miv_simulator.utils.neuron.PRconfig attribute) generate-distance-connections command line option --cache-size --chunk-size --config --config-prefix --connectivity-namespace --connectivity-path --coords-namespace --coords-path --debug --distances-namespace --dry-run --forest-path --include --interp-chunk-size --io-size --resolution --synapses-namespace --value-chunk-size --verbose --write-size -i -v generate-input-features command line option --arena-id --cache-size --chunk-size --config --config-prefix --coords-path --debug --debug-count --distances-namespace --dry-run --fig-format --font-size --gather --interactive --io-size --output-path --plot --populations --save-fig --save-fig-dir --show-fig --value-chunk-size --verbose --write-size -n -p -v generate-input-spike-trains command line option --arena-id --cache-size --chunk-size --config --config-prefix --coords-path --debug --distances-namespace --dry-run --fig-format --font-size --gather --io-size --n-trials --output-path --phase-mod --plot --populations --save-fig --save-fig-dir --selectivity-namespace --selectivity-path --show-fig --spike-train-attr-name --spikes-namespace --value-chunk-size --verbose --write-size -p -v generate-soma-coordinates command line option --alpha-radius --chunk-size --config --config-prefix --dispersion-delta --geometry-path --io-size --nodeiter --output-namespace --output-path --populations --resolution --snap-delta --types-path --value-chunk-size --verbose -i -v generate_connections() (in module miv_simulator.simulator) generate_input_features() (in module miv_simulator.stimulus) generate_input_spike_trains() (in module miv_simulator.stimulus) generate_linear_trajectory() (in module miv_simulator.stimulus) generate_network_architecture() (in module miv_simulator.simulator) generate_synapse_forest() (in module miv_simulator.simulator) generate_synaptic_connections() (in module miv_simulator.connections) generate_uv_distance_connections() (in module miv_simulator.connections) generate_weights() (in module miv_simulator.clamps.network) generator_ifempty() (in module miv_simulator.utils.utils) generator_peek() (in module miv_simulator.utils.utils) get_2D_arena_bounds() (in module miv_simulator.stimulus) get_2D_arena_extents() (in module miv_simulator.stimulus) get_2D_arena_grid() (in module miv_simulator.stimulus) get_2D_arena_spatial_mesh() (in module miv_simulator.stimulus) get_distance_to_node() (in module miv_simulator.cells) get_env_spike_dict() (in module miv_simulator.spikedata) get_filtered_syn_ids() (miv_simulator.synapses.SynapseAttributes method) get_h5py_attr() (in module miv_simulator.utils.io) get_h5py_group() (in module miv_simulator.utils.io) get_inhom_poisson_spike_times_by_thinning() (in module miv_simulator.stgen) get_input_cell_config() (in module miv_simulator.stimulus) get_mech_attrs() (miv_simulator.synapses.SynapseAttributes method) get_netcon() (miv_simulator.synapses.SynapseAttributes method) get_node_attribute() (in module miv_simulator.synapses) get_pps() (miv_simulator.synapses.SynapseAttributes method) get_prob() (miv_simulator.connections.ConnectionProb method) get_R2() (in module miv_simulator.utils.utils) get_syn_filter_dict() (in module miv_simulator.synapses) get_syn_mech_param() (in module miv_simulator.synapses) get_vecstim() (miv_simulator.synapses.SynapseAttributes method) get_volume_distances() (in module miv_simulator.geometry.geometry) global_cm (miv_simulator.utils.neuron.BRKconfig attribute) (miv_simulator.utils.neuron.PRconfig attribute) global_diam (miv_simulator.utils.neuron.BRKconfig attribute) (miv_simulator.utils.neuron.PRconfig attribute) global_oscillation_initial_phases() (in module miv_simulator.stimulus) global_oscillation_phase_pref() (in module miv_simulator.stimulus) global_oscillation_phase_shift() (in module miv_simulator.stimulus) go() (in module miv_simulator.clamps.network) H H5FileManager (class in miv_simulator.utils.io) has_mech_attrs() (miv_simulator.synapses.SynapseAttributes method) has_netcon() (miv_simulator.synapses.SynapseAttributes method) has_pps() (miv_simulator.synapses.SynapseAttributes method) has_vecstim() (miv_simulator.synapses.SynapseAttributes method) hillock (miv_simulator.utils.neuron.HocCellInterface attribute) HocCellInterface (class in miv_simulator.utils.neuron) I ic_constant (miv_simulator.utils.neuron.BRKconfig attribute) (miv_simulator.utils.neuron.PRconfig attribute) icp_transform() (in module miv_simulator.geometry.geometry) ifempty() (in module miv_simulator.utils.utils) import_mech_dict_from_file() (in module miv_simulator.cells) import_morphology_from_hoc() (in module miv_simulator.cells) include() (miv_simulator.utils.utils.IncludeLoader method) IncludeLoader (class in miv_simulator.utils.utils) init() (in module miv_simulator.clamps.network) (in module miv_simulator.network) init_biophys_cell() (in module miv_simulator.clamps.cell) init_biophysics() (in module miv_simulator.cells) init_edge_attrs() (miv_simulator.synapses.SynapseAttributes method) init_edge_attrs_from_iter() (miv_simulator.synapses.SynapseAttributes method) init_input_cells() (in module miv_simulator.network) init_inputs_from_features() (in module miv_simulator.clamps.network) init_inputs_from_spikes() (in module miv_simulator.clamps.network) init_nseg() (in module miv_simulator.utils.neuron) init_spike_detector() (in module miv_simulator.cells) init_syn_id_attrs() (miv_simulator.synapses.SynapseAttributes method) init_syn_id_attrs_from_iter() (miv_simulator.synapses.SynapseAttributes method) init_syn_mech_attrs() (in module miv_simulator.synapses) insert_biophys_cell_syns() (in module miv_simulator.synapses) insert_hoc_cell_syns() (in module miv_simulator.synapses) interp_soma_distances() (in module miv_simulator.geometry.geometry) interplocs() (in module miv_simulator.utils.neuron) interpxyz() (in module miv_simulator.lfp) is_art (miv_simulator.utils.neuron.HocCellInterface attribute) is_cell_registered() (in module miv_simulator.cells) is_reduced (miv_simulator.utils.neuron.HocCellInterface attribute) L lambda_f() (in module miv_simulator.utils.neuron) layers (miv_simulator.env.SynapseConfig attribute) ld_bal() (in module miv_simulator.network) lfpout() (in module miv_simulator.utils.io) list_argsort() (in module miv_simulator.utils.utils) list_find() (in module miv_simulator.utils.utils) list_find_all() (in module miv_simulator.utils.utils) list_index() (in module miv_simulator.utils.utils) load_biophys_cell_dicts() (in module miv_simulator.cells) load_cell_template() (in module miv_simulator.utils.neuron) load_celltypes() (miv_simulator.env.Env method) lpt() (in module miv_simulator.lpt) lpt_bal() (in module miv_simulator.network) Ltotal (miv_simulator.utils.neuron.BRKconfig attribute) (miv_simulator.utils.neuron.PRconfig attribute) M make-h5types command line option --config --config-prefix --gap-junctions --output-path -c make_biophys_cell() (in module miv_simulator.cells) make_BRK_cell() (in module miv_simulator.cells) make_cell_selection() (in module miv_simulator.network) make_cells() (in module miv_simulator.network) make_geometric_graph() (in module miv_simulator.utils.utils) make_hoc_cell() (in module miv_simulator.cells) make_input_cell() (in module miv_simulator.cells) make_input_cell_selection() (in module miv_simulator.network) make_morph_graph() (in module miv_simulator.cells) make_network_volume() (in module miv_simulator.volume) make_neurotree_hoc_cell() (in module miv_simulator.cells) make_PR_cell() (in module miv_simulator.cells) make_random_clusters() (in module miv_simulator.utils.utils) make_rec() (in module miv_simulator.utils.neuron) make_rotate3d() (in module miv_simulator.geometry.geometry) make_SC_cell() (in module miv_simulator.cells) make_section_graph() (in module miv_simulator.cells) make_shared_synapse_mech() (in module miv_simulator.synapses) make_spike_dict() (in module miv_simulator.spikedata) make_syn_mech() (in module miv_simulator.synapses) make_unique_synapse_mech() (in module miv_simulator.synapses) measure-distances command line option --alpha-radius --cache-size --chunk-size --config --config-prefix --coords-namespace --coords-path --geometry-path --io-size --nsample --populations --resolution --value-chunk-size --verbose -i -v measure_deflection() (in module miv_simulator.clamps.cell) measure_distances() (in module miv_simulator.simulator) measure_time_constant() (in module miv_simulator.clamps.cell) mechanisms (miv_simulator.env.SynapseConfig attribute) miv_simulator.cells module miv_simulator.clamps.cell module miv_simulator.clamps.network module miv_simulator.connections module miv_simulator.env module miv_simulator.geometry.alphavol module miv_simulator.geometry.geometry module miv_simulator.geometry.linear_volume module miv_simulator.geometry.point_fit module miv_simulator.geometry.rbf_surface module miv_simulator.geometry.rbf_volume module miv_simulator.lfp module miv_simulator.lpt module miv_simulator.network module miv_simulator.plotting module miv_simulator.spikedata module miv_simulator.statedata module miv_simulator.stgen module miv_simulator.stimulus module miv_simulator.synapses module miv_simulator.utils.io module miv_simulator.utils.neuron module miv_simulator.utils.simtime module miv_simulator.utils.utils module miv_simulator.volume module mkgap() (in module miv_simulator.utils.neuron) mknetcon() (in module miv_simulator.utils.neuron) mknetcon_vecstim() (in module miv_simulator.utils.neuron) mkout() (in module miv_simulator.utils.io) mod_depth (miv_simulator.stimulus.PhaseModConfig attribute) modify_mech_attrs() (miv_simulator.synapses.SynapseAttributes method) modify_syn_param() (in module miv_simulator.synapses) module miv_simulator.cells miv_simulator.clamps.cell miv_simulator.clamps.network miv_simulator.connections miv_simulator.env miv_simulator.geometry.alphavol miv_simulator.geometry.geometry miv_simulator.geometry.linear_volume miv_simulator.geometry.point_fit miv_simulator.geometry.rbf_surface miv_simulator.geometry.rbf_volume miv_simulator.lfp miv_simulator.lpt miv_simulator.network miv_simulator.plotting miv_simulator.spikedata miv_simulator.statedata miv_simulator.stgen miv_simulator.stimulus miv_simulator.synapses miv_simulator.utils.io miv_simulator.utils.neuron miv_simulator.utils.simtime miv_simulator.utils.utils miv_simulator.volume mpi_excepthook() (in module miv_simulator.clamps.network) mvcorrcoef() (in module miv_simulator.utils.utils) N NamedTupleWithDocstring() (in module miv_simulator.utils.utils) NetclampConfig (class in miv_simulator.env) network_volume() (in module miv_simulator.volume) O optimize() (in module miv_simulator.clamps.network) optimize_parameters (miv_simulator.env.NetclampConfig attribute) oscillation_phase_mod_config() (in module miv_simulator.stimulus) P parse_connection_config() (miv_simulator.env.Env method) parse_gapjunction_config() (miv_simulator.env.Env method) parse_netclamp_config() (miv_simulator.env.Env method) partition_syn_ids_by_source() (miv_simulator.synapses.SynapseAttributes method) partition_synapses_by_source() (miv_simulator.synapses.SynapseAttributes method) partitionn() (in module miv_simulator.utils.utils) PCA() (in module miv_simulator.geometry.point_fit) phase_offset (miv_simulator.stimulus.PhaseModConfig attribute) phase_pref (miv_simulator.stimulus.PhaseModConfig attribute) phase_range (miv_simulator.stimulus.PhaseModConfig attribute) PhaseModConfig (class in miv_simulator.stimulus) plot-biophys-cell-tree command line option --bgcolor --colormap --config --config-prefix --data-file --dataset-prefix --font-size --gid --load-synapses --plot-method --population --syn-source-threshold --syn-sources --syn-types --template-paths --verbose -c -g -p -s -v plot-cell-tree command line option --color-edge-scalars --conn-loc --forest-path --gid --line-width --mayavi --no-color-edge-scalars --no-conn-loc --population --verbose -g -i -m -p -v plot-coords-in-volume command line option --config --coords-namespace --coords-path --mayavi --populations --scale --subpopulation --subvol --verbose -c -i -m -n -v plot-network-clamp command line option --all-spike-hist --config-file --config-prefix --exclude-artificial --font-size --gid --include-artificial --input-path --labels --legend --line-width --lowpass-plot-type --n-trials --populations --spike-hist-bin --spike-namespace --state-namespace --state-variable --t-max --t-min --t-variable --target-input-features-arena-id --target-input-features-namespace --target-input-features-path --target-input-features-trajectory-id --verbose -g -i -n -p -v plot-spike-raster command line option --exclude-artificial --fig-size --font-size --include-artificial --labels --max-spikes --populations --save-format --spike-events-namespace --spike-events-path --spike-hist-bin --t-max --t-min --t-variable --verbose -i -n -p -v plot-state command line option --colormap --distance --font-size --gid --lowpass-plot --max-units --populations --query --reduce --state-namespace --state-namespace-pattern --state-path --state-variable --t-max --t-min --t-variable --verbose -g -i -n -p -q -v plot_2D_histogram() (in module miv_simulator.plotting) plot_2D_rate_map() (in module miv_simulator.plotting) plot_biophys_cell_tree() (in module miv_simulator.plotting) plot_coordinates() (in module miv_simulator.plotting) plot_graph() (in module miv_simulator.plotting) plot_intracellular_state() (in module miv_simulator.plotting) plot_lfp() (in module miv_simulator.plotting) plot_lfp_spectrogram() (in module miv_simulator.plotting) plot_network_clamp() (in module miv_simulator.plotting) plot_single_vertex_dist() (in module miv_simulator.plotting) plot_spatial_spike_raster() (in module miv_simulator.plotting) plot_spike_histogram() (in module miv_simulator.plotting) plot_spike_raster() (in module miv_simulator.plotting) points (miv_simulator.geometry.alphavol.AlphaShape attribute) points_plane_fit() (in module miv_simulator.geometry.point_fit) pp (miv_simulator.utils.neuron.BRKconfig attribute) (miv_simulator.utils.neuron.PRconfig attribute) PRconfig (class in miv_simulator.utils.neuron) print_param_dict_like_yaml() (in module miv_simulator.utils.utils) PRneuron (class in miv_simulator.cells) Promise (class in miv_simulator.utils.utils) proportions (miv_simulator.env.SynapseConfig attribute) Q query-cell-attrs command line option --input-path --populations -i -p R random_choice_w_replacement() (in module miv_simulator.utils.utils) random_clustered_shuffle() (in module miv_simulator.utils.utils) rate_maps_from_features() (in module miv_simulator.stimulus) read_from_yaml() (in module miv_simulator.utils.utils) read_spike_events() (in module miv_simulator.spikedata) record_cell() (in module miv_simulator.cells) recsout() (in module miv_simulator.utils.io) register_cell() (in module miv_simulator.cells) reinit_diam() (in module miv_simulator.utils.neuron) report_topology() (in module miv_simulator.cells) reset_cable_by_node() (in module miv_simulator.cells) restore_mech_attrs() (miv_simulator.synapses.SynapseAttributes method) rotate2d() (in module miv_simulator.geometry.geometry) rotate3d() (in module miv_simulator.geometry.geometry) run() (in module miv_simulator.clamps.network) (in module miv_simulator.network) run-network command line option --arena-id --cell-attr-gen-cache-size --cell-selection-path --checkpoint-clear-data --checkpoint-interval --cleanup --config-file --config-prefix --dataset-prefix --debug --dry-run --dt --hoc-lib-path --io-size --ldbal --lptbal --max-walltime-hours --mechanisms-path --microcircuit-inputs --no-cleanup --node-rank-file --output-syn-spike-count --profile-memory --recording-profile --results-id --results-path --results-write-time --spike-input-attr --spike-input-namespace --spike-input-path --stimulus-id --stimulus-onset --template-paths --tstop --use-cell-attr-gen --use-coreneuron --v-init --verbose --write-selection -m -v run_with() (in module miv_simulator.clamps.network) S sample-cells command line option --arena-id --config --config-prefix --dataset-prefix --distances-namespace --input-features-namespaces --input-features-path --io-size --output-path --selection-path --spike-input-attr --spike-input-namespace --spike-input-path --stimulus-id --verbose -c -n -o -v save_figure() (in module miv_simulator.plotting) SCneuron (class in miv_simulator.cells) sections (miv_simulator.env.GapjunctionConfig attribute) (miv_simulator.env.SynapseConfig attribute) (miv_simulator.utils.neuron.HocCellInterface attribute) set_h5py_attr() (in module miv_simulator.utils.io) set_mech_param() (in module miv_simulator.cells) set_syn_mech_param() (in module miv_simulator.synapses) shotnoise_fromspikes() (in module miv_simulator.stgen) show() (in module miv_simulator.clamps.network) show-h5types command line option --input-path -p show_celltypes() (in module miv_simulator.utils.io) shutdown() (in module miv_simulator.network) signal_power_spectrogram() (in module miv_simulator.utils.utils) simplices (miv_simulator.geometry.alphavol.AlphaShape attribute) soma (miv_simulator.utils.neuron.HocCellInterface attribute) soma_alpha_Caconc (miv_simulator.utils.neuron.BRKconfig attribute) soma_f_Caconc (miv_simulator.utils.neuron.BRKconfig attribute) soma_g_pas (miv_simulator.utils.neuron.BRKconfig attribute) (miv_simulator.utils.neuron.PRconfig attribute) soma_gmax_CaN (miv_simulator.utils.neuron.BRKconfig attribute) soma_gmax_K (miv_simulator.utils.neuron.BRKconfig attribute) (miv_simulator.utils.neuron.PRconfig attribute) soma_gmax_KCa (miv_simulator.utils.neuron.BRKconfig attribute) soma_gmax_Na (miv_simulator.utils.neuron.BRKconfig attribute) (miv_simulator.utils.neuron.PRconfig attribute) soma_kCa_Caconc (miv_simulator.utils.neuron.BRKconfig attribute) spatial_phase_mod() (in module miv_simulator.stimulus) spike_density_estimate() (in module miv_simulator.spikedata) spikeout() (in module miv_simulator.utils.io) stash_mech_attrs() (miv_simulator.synapses.SynapseAttributes method) state (miv_simulator.utils.neuron.HocCellInterface attribute) stationary_phase_mod() (in module miv_simulator.stimulus) StimulusConfig (in module miv_simulator.env) syn_in_seg() (in module miv_simulator.synapses) synapse_seg_counts() (in module miv_simulator.synapses) synapse_seg_density() (in module miv_simulator.synapses) SynapseAttributes (class in miv_simulator.synapses) SynapseConfig (class in miv_simulator.env) SynapseSource (class in miv_simulator.synapses) T template_params (miv_simulator.env.NetclampConfig attribute) transform_volume() (in module miv_simulator.geometry.geometry) tri_graph() (in module miv_simulator.geometry.alphavol) type (miv_simulator.env.SynapseConfig attribute) U update() (miv_simulator.utils.utils.Context method) update_biophysics_by_sec_type() (in module miv_simulator.cells) update_mechanism_by_node() (in module miv_simulator.cells) update_syn_mech_by_sec_type() (in module miv_simulator.synapses) update_syn_mech_param_by_sec_type() (in module miv_simulator.synapses) V V_rest (miv_simulator.utils.neuron.BRKconfig attribute) (miv_simulator.utils.neuron.PRconfig attribute) V_threshold (miv_simulator.utils.neuron.BRKconfig attribute) (miv_simulator.utils.neuron.PRconfig attribute) validate_syn_mech_param() (in module miv_simulator.synapses) viewvalues() (in module miv_simulator.utils.utils) volumes() (in module miv_simulator.geometry.alphavol) W weight_generators (miv_simulator.env.NetclampConfig attribute) write_cell_selection() (in module miv_simulator.utils.io) write_connection_selection() (in module miv_simulator.utils.io) write_input_cell_selection() (in module miv_simulator.utils.io) write_syn_spike_count() (in module miv_simulator.synapses) write_to_yaml() (in module miv_simulator.utils.utils) Y yaml_convert_scalars() (in module miv_simulator.utils.utils)