| abs_tol |
Absolute tolerance for ODE integration |
| absolute_value |
Absolute value of the score at the time of assessment |
| accelerator |
Hardware accelerator the run targets |
| account |
Accounting allocation to charge the tasks against (Slurm) |
| acquisition |
Acquisition protocol or scanner information |
| acronym |
|
| acted_on_behalf_of |
Packages whose use triggered this one, so a backend invoked through a framewo… |
| active_contacts |
|
| activities |
The runs that produced this artifact, serialized to BEP028’s activity record |
| add |
Recurrence folding one arriving sample v into the state |
| additional_equations |
|
| additive |
Indicates whether the noise is additive |
| affect |
Affect function: what happens when the event triggers |
| affect_negative |
Affect on downcrossing (continuous events only) |
| affect_parameters |
Parameter symbols modifiable in the affect function |
| affect_states |
State variable symbols modifiable in the affect function |
| age |
Age at time of study (years) |
| aggregate |
How to aggregate the result across dimensions |
| aggregation |
How to aggregate over time |
| algorithm |
Checksum function name, e |
| algorithms |
Names of the experiment’s algorithms (keys in experiment | | [allow_self_connections](slots/allow_self_connections.qmd) | For a self-projection (source and target are the same population) expanded un... | | [alternative_identifier](slots/alternative_identifier.qmd) | Further identifiers for the same package, an RRID among them (BEP028 ``Altern... | | [amplitude](slots/amplitude.qmd) | | | [analyses](slots/analyses.qmd) | Analyses of this study's results, each persisted as its own container and so ... | | [analysis](slots/analysis.qmd) | WHERE (short form): an in-study analysis name whose saved result holds the ar... | | [anatomicalAxesOrientation](slots/anatomicalAxesOrientation.qmd) | Add the axes orientation in standard anatomical terms (XYZ) | | [animation](slots/animation.qmd) | Turns the figure into a movie over one dimension of its data instead of a sti... | | [annotations](slots/annotations.qmd) | Positioned text labels drawn on the panel (e | | [application_category](slots/application_category.qmd) | High-level category (e | | [apply_every](slots/apply_every.qmd) | Apply update every N iterations | | [apply_on_dimension](slots/apply_on_dimension.qmd) | Which dimension to apply the transformation on | | [archive](slots/archive.qmd) | How to package the run into a COMBINE/OMEX archive — the single supplementary... | | [args](slots/args.qmd) | Ordered parameter names passed to the callable | | [arguments](slots/arguments.qmd) | Variables consumed by the function (referenced in the equation), keyed by arg... | | [array_chunk](slots/array_chunk.qmd) | Overrides ``distribute | | [arrow](slots/arrow.qmd) | Draw an arrow POINTING AT (x, y), starting (dx, dy) away from it in axes frac... | | [aspect](slots/aspect.qmd) | The DATA aspect ratio:equal— one unit of x is one unit of y, what a matri... | | [associated_with](slots/associated_with.qmd) | The software that carried the activity out (BEP028 ``AssociatedWith``) | | [at](slots/at.qmd) | Where the rule sits: one value for a horizontal or vertical rule,[slope, in… |
| atlas |
The parcellation the layer’s per-region values are placed through, BY LABEL —… |
| author |
Original author(s) or creating organization(s) |
| authors |
Author display strings (full detail in references |
| auto_format |
Apply bsplot’s format_fig (tick/label normalisation + panel numbers) |
| autonomous |
Whether the system is autonomous (equations do not depend explicitly on time … |
| aux_data |
Ordered list of auxiliary inputs the observation pipeline consumes |
| average |
Averaging mode across trials |
| axesOrigin |
Enter the origin (central point where all axes intersect) |
| axis |
Array axis a normalize step reduces over (0 = columns) |
| axis_width |
Line weight of the axes frame, in points |
| azimuth |
Angle around the vertical axis, in degrees |
| backend |
Execution backend this experiment runs on when no backend is passed explicitl… |
| backends |
Codegen backends this recipe is registered for; others recompute |
| background |
The page the figure is printed on |
| base |
Standard lines, bars and markers, wherever the colour carries no meaning |
| baseline_value |
Preoperative baseline value of the score |
| batch_mode |
How the per-subject fits are executed |
| batch_size |
On-device chunk width — how many subjects form one vectorised batch |
| bc_type |
|
| between |
Text written in the gap BEFORE each cell, which is what turns a row of maps i… |
| bids |
Standing with the BIDS standard |
| bids_dir |
Path to BEP017-compliant BIDS directory for loading connectivity matrices |
| bids_root |
Path to BIDS dataset root directory |
| bids_version |
BIDS version the layout was written against |
| bindings |
Per-backend construction bindings, keyed by backend id (e |
| block_size |
Streaming-fold granularity: how many integration steps form one block that is… |
| bothside |
Continue branch in both directions |
| bottom |
Strip reserved at the bottom for the cells’ tick labels or a shared axis labe… |
| boundary_conditions |
|
| bounds |
[x0, y0, width, height] in host-axes fractions, as matplotlib’s inset_axes ta… |
| box_aspect |
The frame’s height over its width, independent of the data ranges: a square p… |
| branches |
Child branches to continue from detected bifurcation points (PO from Hopf, fo… |
| build_hash |
Deterministic hash of the resolved dependency set |
| builder |
Optional Python callable that builds the network at YAML load time |
| bundle |
When true, emitting a self-contained kit copies this dataset’s per-subject fi… |
| by |
Default tier for axes not named in vectorize or workflow |
| call_args |
Arguments passed when calling the instance (call) |
| callable |
Name of the constructor function in the library |
| camera |
Viewpoint for a 3-D panel or a surface |
| category |
Coarse classification of the phenotype bundle, used for filtering in larger s… |
| center |
Add the center coordinate of this entity |
| checkpoint_interval |
Gradient-checkpointing interval in milliseconds (backward-pass memory/time tr… |
| chunk |
Sharding granularity — the inter-task (inter-node) tier |
| citation |
Additional citation strings or DOIs |
| citekey |
BibTeX citation key; the join key into references |
| class_call |
Class instantiation and call (alternative to callable/function) |
| class_reference |
Direct class reference (alternative to pipeline) |
| clinical_improvement |
Observed improvement relative to baseline based on a defined score |
| clinical_scores |
|
| clip |
[x, y, width, height] in CSS pixels to crop the capture to a region of the pa… |
| code_modules |
Importable module names whose import registers this figure’s custom panels / … |
| code_source |
Where this study’s callable code lives — the builders and transform/observati… |
| codegen_format |
Export-registry key of the format TVBO emits for this tool (tvbo formats) |
| coefficient |
|
| cohort |
Cohort label (e |
| col_label_pad |
Gap between a column heading and the cells under it |
| col_label_size |
Type size of the column headings |
| col_labels |
One heading per column, written just above the cells rather than at the panel… |
| color |
Add the color code used for visual representation of this entity |
| colorbar |
The colour scale printed beside this panel’s field |
| colormap |
Named colormap (routed through the cmap resolver) |
| colormaps |
The continuous scales, so both kinds of colour move together and no figure na… |
| colors |
One colour per entry of a standalone legend, as a palette role, a hue or any … |
| columns |
How many columns the entries are laid out in |
| command |
The command performed, parameters included |
| comment |
|
| comparison |
Comparison a stochastic_mask applies between of and the draw |
| compile |
Code-generation hint (opt-in, backend-independent): request that the generate… |
| concept_iri |
Cognitive Atlas IRI of the cognitive construct measured (e |
| condition |
Experimental condition label (e |
| condition_parameters |
Parameter symbols accessible in the condition function |
| condition_states |
State variable symbols accessible in the condition function |
| conditionals |
Conditional logic for piecewise equations — the one place a piecewise definit… |
| conditions |
Global condition labels applied across all subjects (e |
| connectivity |
Connectivity rule for a population-level Edge |
| connectivity_ref |
Reference to connectivity data (_conndata-network_connectivity |
| connectome |
A tvbo Network whose companion carries a mesh group |
| constructor_args |
Arguments passed to init when instantiating the class |
| contact_id |
Identifier (e |
| contacts |
List of physical contacts along the electrode |
| container |
Path of the container this record describes, relative to the study root, so t… |
| container_args |
Additional arguments passed verbatim to the container runtime when it execute… |
| container_binds |
Host paths that must be visible inside the container beyond the ones its runt… |
| container_image |
Container image reference (e |
| continuation |
Override solver settings for this branch |
| continuations |
Numerical continuation and bifurcation analysis specifications |
| coordinate |
3D coordinate of the contact center in the defined coordinate space |
| coordinate_space |
|
| coordinates |
Node coordinates (x,y,z) in the given coordinate space |
| cores |
Total cores for local engines (Snakemake –cores) |
| correlated |
Deprecated |
| correlated_over |
Which axis covariance indexes — node (equivalently region) for spatiall… |
| correlation |
|
| count |
A structural tally computed from the specification, not a run: <study> | | [coupling](slots/coupling.qmd) | How activity travels along this network's connections — the one place a coupl... | | [coupling_evaluation](slots/coupling_evaluation.qmd) | Backend-neutral numerical treatment of the network coupling term across the s... | | [coupling_function](slots/coupling_function.qmd) | Mathematical function defining the coupling | | [coupling_inputs](slots/coupling_inputs.qmd) | | | [coupling_variable](slots/coupling_variable.qmd) | Whether this state variable is transmitted to connected nodes through the cou... | | [covariance](slots/covariance.qmd) | Covariance of the unit-intensity noise increment across the axis named by `co... | | [cpus_per_task](slots/cpus_per_task.qmd) | CPU cores requested per task (Slurm --cpus-per-task) | | [cse](slots/cse.qmd) | Code-generation hint (opt-in, backend-independent): eliminate common subexpre... | | [curvature](slots/curvature.qmd) | Optional path to per-vertex curvature (N,) float | | [dash](slots/dash.qmd) | Dash pattern (`solid`, `dashed`, `dotted`, `dashdot`) | | [data](slots/data.qmd) | | | [data_file](slots/data_file.qmd) | Path to the h5 companion (relative to the yaml) | | [data_source](slots/data_source.qmd) | | | [dataLocation](slots/dataLocation.qmd) | | | [dataset](slots/dataset.qmd) | Multi-subject dataset for workflow rendering | | [dataset_id](slots/dataset_id.qmd) | Unique identifier for this phenotype bundle | | [dataset_type](slots/dataset_type.qmd) | BIDSDatasetTypethis layout realises, written into the dataset'sdatas… |
| datatype |
Declared value type of this parameter, given as a schema range name — a primi… |
| date_created |
Date the software was first released (YYYY-MM-DD) |
| date_modified |
Date of the most recent release or significant update |
| decimals |
How many decimal places the tick numbers are written to |
| default |
|
| defaultImage |
Add all image files used as visual representation of this common coordinate s… |
| definition |
|
| degree |
Polynomial degree per mesh interval for collocation |
| delay |
Conduction delay (explicit edges, ms) |
| delayed |
|
| delta_p |
Initial parameter offset from the bifurcation point |
| density |
The template’s vertex density (164k) |
| depends_on |
Upstream task whose result seeds this optimization |
| derivative_initial_value |
Initial value for the first time derivative, used when equation_order > 1 |
| derived_from |
|
| derived_from_model |
|
| derived_parameters |
|
| derived_variables |
|
| desc |
BIDS desc- entity (e |
| description |
|
| descriptor |
Short alphanumeric identifier for the BIDS desc- filename entity (e |
| detail |
Non-visual grouping dim (e |
| detect_bifurcation |
Bifurcation detection level |
| detect_fold |
Enable fold (limit point) detection |
| development_status |
Development status (repostatus |
| device_scale_factor |
Device pixel ratio; 2-3 renders a crisp raster at print resolution (the brows… |
| diagnosis |
|
| diagonal |
Value written onto the diagonal of a pairwise_distance result, e |
| differentiation |
Backend-neutral strategy for propagating gradients through the temporal integ… |
| digest |
Checksums of the artifact itself, keyed by function name |
| dimension |
The tool’s name for the physical dimension of this unit |
| dimension_labels |
Ordered labels for the matrix columns (dim-1) when the matrix is non-square |
| dims |
Axis names of this observation’s output, outermost first, e |
| directed |
Whether to generate a directed graph |
| direction |
Exceedance direction: greater_equal (fraction of permutations whose stati… |
| discretization |
Discretization method for the branch solution |
| distance |
Edge length / tract distance (explicit edges, mm) |
| distance_unit |
Unit for distances/lengths in the network |
| distribute |
How exploration axes map onto the vectorized vs fanned-out tiers |
| distribution |
Distribution sampled by a sample / stochastic_mask step, or whose density… |
| diverging |
Signed quantities read against a midpoint, where the two directions must be t… |
| doi |
Digital Object Identifier for the software or its reference publication |
| domain |
|
| downsample_period |
Intermediate downsampling period (ms) |
| dpi |
Raster resolution (dots per inch); scales pixel output only, not the physical… |
| ds |
Initial arc-length step size |
| ds_max |
Maximum adaptive step size |
| ds_min |
Minimum adaptive step size |
| dtype |
Data type the matrix values are stored as |
| duration |
|
| dynamics |
Dictionary of dynamics models keyed by name |
| ecosystem |
Package ecosystem(s) through which the software is distributed |
| edge_alpha |
Opacity of those connections |
| edge_color |
Draw the triangulation in this colour, for a panel whose subject is the mesh … |
| edge_matrix_files |
|
| edge_percentile |
Keep only edges above this percentile of the weights |
| edge_template |
Default Edge attributes applied to every Edge in this Network |
| edge_width |
Line weight of the triangulation |
| edges |
List of directed edges with coupling references (optional, for explicit edge … |
| efield |
Metadata about the E-field result for this setting |
| electrode_id |
Unique identifier for this electrode |
| electrode_reference |
|
| electrodes |
|
| element |
Element/node index this range applies to |
| element_domains |
Per-element domain overrides for heterogeneous parameters |
| element_type |
|
| elements |
Topology indices: either a file reference, or (when inlined on a Network) a d… |
| elevation |
Angle above the horizontal plane, in degrees |
| emit |
Expression reading the reduced value out of the state |
| emit_kind |
Whether the reduced value is read out every step or every stride |
| empirical_data |
Paths to empirical recordings for this session (e |
| encoding |
|
| ended_at |
ISO 8601 end time |
| enforce |
For a state-variable domain: whether/how to enforce the range during inte… |
| engine |
Primary engine (must appear in environment |
| entities |
|
| env |
Environment variables exported before the task command on every engine (e |
| environment |
|
| environment_type |
Category: conda, venv, docker, etc |
| equation |
|
| equation_order |
Order of the time derivative on the LHS |
| equation_type |
How to interpret equation | | [evaluate](slots/evaluate.qmd) | Materialise this algorithm's post-tuning evaluation: a simulation of the tune... | | [evaluator](slots/evaluator.qmd) | Who performed the rating (e | | [event_type](slots/event_type.qmd) | Type of event trigger mechanism | | [events](slots/events.qmd) | Events attached to this node (e | | [evict](slots/evict.qmd) | Recurrence taking one leaving sample `v` back out of the state | | [evict_equation](slots/evict_equation.qmd) | Optional reverse recurrence for a **sliding-window** reduction: the per-step ... | | [execution](slots/execution.qmd) | Which backend renders this analysis, and at what precision / accelerator / wo... | | [executor](slots/executor.qmd) | Executor to run the pipeline through (Nextflow process | | [experiment](slots/experiment.qmd) | WHERE (short form): an in-study experiment id whose saved result holds the ar... | | [experiment_yaml_hash](slots/experiment_yaml_hash.qmd) | SHA-256 hex digest of the normalised experiment YAML that produced this artif... | | [expires_with](slots/expires_with.qmd) | For an unsanctioned or proposed directory, what would retire its |
| explorations |
Parameter exploration/grid search specifications |
| explored_values |
Explicit explored values for this element |
| expression |
The equation to apply when the condition is met |
| extension |
|
| family_wise |
Apply a Westfall–Young family-wise (max-T) correction: collapse the permuted … |
| field |
Dotted-path subkey within the referenced entity (optional) |
| field_dynamics |
|
| figures |
Declarative Figure specs rendered from this study’s experiment results — clos… |
| file |
|
| files |
Files at the dataset root |
| fill |
Fill the rectangle rather than outlining it |
| fill_cell |
Keep the position the layout engine gave this panel, rather than letting a la… |
| find_fixpoint |
Whether to find a fixed point (steady state) before time integration |
| font_family |
The typefaces to set text in, most-wanted first ([Helvetica, Arial, DejaVu S... | | [font_size](slots/font_size.qmd) | Base font size in points (physical: 1 pt = 1/72 inch) | | [format](slots/format.qmd) | Output format (pdf/svg/png) | | [fps](slots/fps.qmd) | Playback rate of the saved movie in frames per second (default 20) | | [fraction](slots/fraction.qmd) | Width of the bar as a fraction of the panel | | [frame](slots/frame.qmd) | Whether the panel keeps its frame and its ticks | | [frames](slots/frames.qmd) | How many frames to draw | | [free](slots/free.qmd) | | | [free_parameters](slots/free_parameters.qmd) | Parameters to optimize in this stage | | [freeze_parameters](slots/freeze_parameters.qmd) | Parameters from previous stages to freeze (keep at optimized value but not up... | | [frequency](slots/frequency.qmd) | | | [function](slots/function.qmd) | Custom distribution function (PDF or sampling callable) | | [functions](slots/functions.qmd) | | | [funder](slots/funder.qmd) | Funding bodies or grants (e | | [gather](slots/gather.qmd) | Observer parameter ``(n_groups, n)`` of node indices selecting each group's n... | | [gaussian](slots/gaussian.qmd) | Indicates whether the noise is Gaussian | | [generated](slots/generated.qmd) | Written by tooling and overwritten on the next run, so it is never hand-edite... | | [generated_at](slots/generated_at.qmd) | Timestamp when this TimeSeries was generated | | [generated_by](slots/generated_by.qmd) | Software/agent identifier: the prov:Agent this artifact is attributed to | | [geometry](slots/geometry.qmd) | Read the layer as (V, 3) vertex COORDINATES rather than as a field: what the ... | | [git](slots/git.qmd) | Git repository URL to fetch the code from (shallow-cloned and cached under ``... | | [graph_generator](slots/graph_generator.qmd) | Graph generator specification | | [graph_representation](slots/graph_representation.qmd) | Representation used to evaluate coupling over this network's connectivity (``... | | [gres](slots/gres.qmd) | Generic scheduler resources, e | | [grid](slots/grid.qmd) | How akind: gridpanel tiles its cells | | [grid_lines](slots/grid_lines.qmd) | Draw the axes grid | | [grounding](slots/grounding.qmd) | External ontology IRIs (typically GO, ChEBI, UBERON, CL, MeSH) that this enti... | | [group](slots/group.qmd) | Group assignment (e | | [groups](slots/groups.qmd) | | | [ha](slots/ha.qmd) | Horizontal alignment against (x, y) — left, center, right | | [handedness](slots/handedness.qmd) | | | [handle_length](slots/handle_length.qmd) | Length of each entry's sample line | | [has_reference](slots/has_reference.qmd) | | | [hash](slots/hash.qmd) | Build or artifact hash for exact reproducibility | | [head](slots/head.qmd) | | | [height](slots/height.qmd) | Figure height in mm (physical print size) | | [height_ratios](slots/height_ratios.qmd) | Relative heights of the mosaic rows, e | | [hemi](slots/hemi.qmd) | Which hemisphere to draw (left,right, orbothjoined into one mesh — w... | | [hemisphere](slots/hemisphere.qmd) | Add the hemisphere of this entity | | [heterogeneous](slots/heterogeneous.qmd) | | | [hi](slots/hi.qmd) | Upper bound or stopping value | | [hide_xticklabels](slots/hide_xticklabels.qmd) | Draw the x ticks without their numbers | | [hide_yticklabels](slots/hide_yticklabels.qmd) | Draw the y ticks without their numbers | | [highlight](slots/highlight.qmd) | The single emphasis colour, kept out of the cycler so it never lands on a pan... | | [histogram](slots/histogram.qmd) | Bin spec (lo,hi,n) for a streaming order-statistic aggregation (aggr… |
| history |
|
| homepage |
Project homepage URL |
| hspace |
Gap between rows, in the same fraction |
| hyperparameters |
Stage-specific hyperparameters (e |
| id |
Unique node identifier |
| image |
A dseg segmentation file, for a parcellation nobody has curated |
| imaging_modality |
Type of imaging modality (BOLD, EEG, MEG, etc |
| in_templates |
Init templates that include this directory |
| include |
Extra file globs to add beyond the recipes, derived containers, figures and m… |
| includes |
Include update rules from other algorithms with optional argument overrides |
| incoming_states |
References to state variables from connected (source) nodes |
| inferences |
Bayesian inference configurations (posterior over parameters given an observa… |
| initial_expression |
Analytic initial condition for the field |
| initial_state |
How to obtain the initial equilibrium |
| initial_value |
Value this state starts at |
| ink |
Text, spines and ticks: the near-black everything is read against |
| inner_coupling |
For hierarchical coupling: inner coupling applied at regional level |
| inner_iterations |
For mode=nested only: number of inner-loop iterations to run per outer iterat… |
| input |
Simple input reference: name of previous function’s output in pipeline |
| inputs |
Per-input fingerprints for cache invalidation |
| insets |
Sub-axes drawn inside this panel after its own body — the zoom windows, corne… |
| integration |
Clock this network’s nodes run on |
| intensity_projection |
How voxels collapse along the view axis (absmax by default) |
| intermediate_expressions |
|
| interoperates_with |
Tools this tool can exchange data with or delegate to |
| interpolate_delays |
For delayed coupling: read delayed states by linear interpolation between the… |
| interpolation |
Interpolation for a data-driven stimulus: ‘linear’ or ‘cubic’ |
| invert_x |
Draw the x axis descending |
| invert_y |
Draw the y axis descending — the matrix convention, row 0 at the top |
| invert_z |
Draw the depth axis of a 3-D panel descending |
| iri |
Optional stable IRI (or compact URI) for this entity in an external ontology … |
| is_accessible_for_free |
Whether the tool is free/open-source |
| issue_tracker |
URL of the bug tracker or issue board |
| jobs |
Concurrent jobs the workflow engine keeps in flight (Snakemake --jobs, wr… |
| key |
Key/variable name within the file (for |
| keys |
Named keys for multi-dimensional coupling |
| keywords |
Tags for topic-based discovery and clustering |
| kind |
|
| label |
|
| label_pad |
Distance from an axis label to its axis, in points |
| labels |
Annotate each node with its region name |
| labels_dimensions |
Mapping of dimension names to their labels (JSON-encoded dict) |
| labels_ordering |
Ordering of dimensions: Time, State Variable, Space, Mode |
| latex |
|
| layers |
Marks sharing this panel’s axes (overlay) |
| layout |
bsplot mosaic string; letters = panel keys, slash (or newline) = new row, rep… |
| layout_engine |
Which layout engine positions the panels |
| learning_rate |
|
| learning_rate_schedule |
Learning rate schedule: ‘constant’, ‘linear’, ‘exponential’ |
| learning_rate_warmup |
Linear warmup of learning rate from 0 to learning_rate over n_iterations |
| left |
Strip reserved at the left for the row labels, as a fraction of the panel |
| legend |
A key for this panel’s own marks |
| legend_frame |
Draw the box around a legend |
| legend_handle_length |
Length of a legend’s sample line, in font-size units |
| legend_pad |
Distance from a legend to the axes it sits against, in font-size units |
| level |
Whether a study MUST, SHOULD or MAY have this directory |
| lhs |
|
| library |
Native library/module providing the callable |
| license |
SPDX license identifier (e |
| likelihood |
Observation model p(data |
| line_width |
Default weight of a drawn line, in points, for any layer whose own style does… |
| linear_solver |
Linear solver for the Newton bordered system |
| linestyles |
One dash pattern per entry of a standalone legend |
| lo |
Lower bound or starting value |
| loader |
Callable that loads the data (e |
| loc |
Named corner (‘upper right’, ‘upper left’, ‘center’, |
| local |
Marks this as a LOCAL (surface/local-connectivity) coupling term rather than … |
| local_coupling_term |
|
| local_states |
References to state variables from the local (target) node |
| location |
Which side of the panel it sits on |
| log_scale |
Whether to use logarithmic spacing |
| loss |
Loss function call |
| mail_type |
Scheduler notification trigger (e |
| mail_user |
Notification email address |
| maintainer |
Current maintainer(s) or responsible organization(s) |
| manufacturer |
|
| mark |
Cartesian mark; omitted for heatmap panels (implied by the panel kind) |
| marker_size |
Default marker size, in points, for any layer whose own style does not fix on… |
| markers |
One marker per entry of a standalone legend, for a key whose entries are scat… |
| mask |
A per-vertex 0/1 file |
| max_bisection_steps |
Maximum bisection steps for bifurcation point localization |
| max_iterations |
|
| max_steps |
Maximum continuation steps |
| measure |
WHICH array to select out of source |
| measure_specs |
Optional per-measure metadata (Cognitive Atlas IRIs, units, description) |
| measure_type |
Sub-type within the phenotype (e |
| measures |
Names of the measures present in the h5 companion (one measures/<name> da… |
| mem |
Memory per task in scheduler syntax (e |
| mesh |
A surface mesh file — GIFTI, VTK, FreeSurfer, or an | | [mesh_file](slots/mesh_file.qmd) | Path to external mesh file (GIFTI, VTK, MSH, FreeSurfer, etc | | [mesh_format](slots/mesh_format.qmd) | The mesh file's format, where the extension does not say | | [mesh_intervals](slots/mesh_intervals.qmd) | Number of mesh intervals (time slices) for collocation or trapezoid methods | | [metadata](slots/metadata.qmd) | Additional subject metadata as key-value pairs or path to a sidecar JSON file | | [method](slots/method.qmd) | Discretization method | | [metric](slots/metric.qmd) | Metric equation for matching (e | | [min_coverage](slots/min_coverage.qmd) | Minimum fraction of the model network's nodes that a ``by_label`` reconciliat... | | [minor_tick_length](slots/minor_tick_length.qmd) | Length of a minor tick mark, in points | | [minor_tick_width](slots/minor_tick_width.qmd) | Line weight of a minor tick mark, in points | | [minor_ticks](slots/minor_ticks.qmd) | Draw minor tick marks between the major ones | | [modality](slots/modality.qmd) | Imaging modality or simulation output type | | [mode](slots/mode.qmd) | | | [model](slots/model.qmd) | | | [model_equation_ref](slots/model_equation_ref.qmd) | BIDS ModelEq reference: path to _eq | | [model_paradigm](slots/model_paradigm.qmd) | Computational paradigms supported | | [model_param_ref](slots/model_param_ref.qmd) | BIDS ModelParam reference: path to _param | | [model_type](slots/model_type.qmd) | Coarse classification of this model (mean_field, neural_mass, phase_oscillato... | | [modes](slots/modes.qmd) | | | [modified](slots/modified.qmd) | | | [module](slots/module.qmd) | | | [modules](slots/modules.qmd) | (Deprecated) Use environment | | [mtime](slots/mtime.qmd) | File modification time at fingerprinting (POSIX timestamp) | | [muted](slots/muted.qmd) | Hairlines and de-emphasised strokes: present, and not competing | | [n](slots/n.qmd) | Number of points (alternative to step for grid exploration) | | [n_inversion](slots/n_inversion.qmd) | Number of eigenvalue sign inversions to flag a bifurcation | | [n_iterations](slots/n_iterations.qmd) | Number of outer iterations to run in this stage | | [n_parallel](slots/n_parallel.qmd) | Grid batch size for parameter exploration — how many sweep cells the backend ... | | [n_regions](slots/n_regions.qmd) | Total number of regions | | [n_sections](slots/n_sections.qmd) | Number of shooting sections for shooting or Poincaré methods | | [n_threads](slots/n_threads.qmd) | Number of CPU threads per worker (-1 = auto-detect) | | [n_trials](slots/n_trials.qmd) | Number of independent trials per grid point | | [n_vertices](slots/n_vertices.qmd) | Total number of vertices | | [n_workers](slots/n_workers.qmd) | Number of parallel workers (maps to pmap devices in JAX, processes in multipr... | | [name](slots/name.qmd) | Full name of the scale (e | | [nativeUnit](slots/nativeUnit.qmd) | Add the native unit that is used for this common coordinate space version | | [nbins](slots/nbins.qmd) | Upper bound on the number of ticks per axis | | [ncols](slots/ncols.qmd) | Cells per row | | [network](slots/network.qmd) | Path to subject-specific connectome (when not session-dependent) | | [nev](slots/nev.qmd) | Number of eigenvalues to compute | | [newton_max_iterations](slots/newton_max_iterations.qmd) | Maximum Newton corrector iterations per step | | [newton_tol](slots/newton_tol.qmd) | Absolute tolerance for Newton corrector convergence | | [nextflow](slots/nextflow.qmd) | Nextflow execution directives | | [node_edge_color](slots/node_edge_color.qmd) | Outline colour of the region markers | | [node_edge_width](slots/node_edge_width.qmd) | Outline weight of the region markers | | [node_mapping](slots/node_mapping.qmd) | HDF5 dataset path for node-to-parent mapping | | [node_size](slots/node_size.qmd) | Marker size for the regions | | [node_template](slots/node_template.qmd) | Default Node attributes applied to every Node in this Network | | [nodes](slots/nodes.qmd) | Network nodes a stimulus-type event is applied to (node ids / indices) | | [noise](slots/noise.qmd) | Optional stochastic contribution to the stimulus | | [noise_draw](slots/noise_draw.qmd) | How the base solve draws its noise realization, and therefore WHICH realizati... | | [noise_type](slots/noise_type.qmd) | Temporal character of the process:gaussian/white(delta-correlated in ti... | | [non_negative](slots/non_negative.qmd) | All values >= 0 | | [normals](slots/normals.qmd) | Optional path inside the parent Network's h5 (or an external file) to per-ver... | | [not_in_templates](slots/not_in_templates.qmd) | Init templates that do *not* get this directory, though every other kind does | | [notes](slots/notes.qmd) | | | [nrows](slots/nrows.qmd) | Rows to fill | | [num_chains](slots/num_chains.qmd) | Independent MCMC chains | | [num_samples](slots/num_samples.qmd) | Posterior samples to draw | | [num_warmup](slots/num_warmup.qmd) | Warmup/adaptation steps before sampling | | [number](slots/number.qmd) | The panel letter to draw, overriding the mosaic key, or the string 'false' to... | | [number_loc](slots/number_loc.qmd) | Per-panel override of the figure's panel_number_loc — e | | [number_of_elements](slots/number_of_elements.qmd) | Number of elements (triangles, quads, tetrahedra, etc | | [number_of_modes](slots/number_of_modes.qmd) | | | [number_of_nodes](slots/number_of_nodes.qmd) | Number of nodes in the network (derived from nodes if not set) | | [number_of_stages](slots/number_of_stages.qmd) | | | [number_of_subjects](slots/number_of_subjects.qmd) | Number of subjects in the tractography dataset | | [number_of_vertices](slots/number_of_vertices.qmd) | Number of vertices in the mesh | | [objective](slots/objective.qmd) | What the algorithm optimizes for | | [objectives](slots/objectives.qmd) | Names of observations minimised by an adaptivestrategy(e | | [observable](slots/observable.qmd) | Observable to compute at each point | | [observational_measures](slots/observational_measures.qmd) | BEP017 measure names for observational targets (e | | [observations](slots/observations.qmd) | References to observations defined in the observations section | | [observed](slots/observed.qmd) | Observable functions computed from states, inputs, and parameters after simul... | | [ode_solver](slots/ode_solver.qmd) | ODE solver for flow-based methods (shooting, poincaré) | | [of](slots/of.qmd) | Name of the input this step consumes — the positions forpairwise_distance... | | [on_region](slots/on_region.qmd) | Mesh/atlas subset where BC applies | | [opacity](slots/opacity.qmd) | | | [opaque](slots/opaque.qmd) | BIDS: the standard does not specify the contents, so a validator does not rea... | | [operating_system](slots/operating_system.qmd) | Supported operating systems (e | | [operator_type](slots/operator_type.qmd) | | | [operators](slots/operators.qmd) | | | [optimizations](slots/optimizations.qmd) | Parameter optimization configurations | | [optional](slots/optional.qmd) | | | [options](slots/options.qmd) | Toolkit-specific string options (jacobian type, etc | | [opts](slots/opts.qmd) | The keyword options of acustomcallable, and of the kinds that carry their... | | [orientation](slots/orientation.qmd) | Which way the bar runs | | [originalLookupLabel](slots/originalLookupLabel.qmd) | Add the original label of this entity as defined in the parcellation terminol... | | [out_dir](slots/out_dir.qmd) | Output directory template | | [output](slots/output.qmd) | WHICH array to take from the container at ``experiment`` / ``iri``: a recorde... | | [output_equation](slots/output_equation.qmd) | Output transformation equation (if equation-based) | | [outputs](slots/outputs.qmd) | The data variables the container actually holds, read off it when the record ... | | [outsym](slots/outsym.qmd) | Output symbol names for the edge model | | [over](slots/over.qmd) | The dimension the frames advance along, by NAME (e | | [package](slots/package.qmd) | Reference to the software package identity | | [pad](slots/pad.qmd) | Whitespace left around the content when trimming, in inches | | [palette](slots/palette.qmd) | The categorical hues, reached into only where a panel separates conditions | | [panel_key](slots/panel_key.qmd) | Mosaic label this panel binds to (matches a letter in Figure | | [panel_number_format](slots/panel_number_format.qmd) | Python format string applied to each panel letter: '{}' -> 'a', '({})' -> '(a... | | [panel_number_loc](slots/panel_number_loc.qmd) | Which corner the panel letter sits in | | [panel_number_offset](slots/panel_number_offset.qmd) | [dx, dy] shift of every panel letter from its corner, in axes fractions | | [panel_number_size](slots/panel_number_size.qmd) | Panel-letter size in points | | [panel_numbers](slots/panel_numbers.qmd) | Draw automatic panel letters (a, b, | | [panels](slots/panels.qmd) | Panels keyed by their mosaic label | | [parallel_batch_size](slots/parallel_batch_size.qmd) | Chunk size for ``lax_map`` and chunked-``vmap`` modes | | [parallel_mode](slots/parallel_mode.qmd) | How trial-axis parallelism is realised at codegen time | | [parameter](slots/parameter.qmd) | Dotted reference to the quantity being swept; also the key of the enclosing… |
| parameters |
|
| parcel_map_field |
When the mesh is inlined on a Network with a parcellation, the dotted path in… |
| parcellation |
Brain parcellation/atlas reference |
| parent_network |
Path/URI to parent (coarser) Network |
| parent_score |
If this score is a subscore of a broader composite |
| partition |
Marks a grouped streaming reduction over a node partition (e |
| path |
External image file (image kind) |
| percent_change |
Percent change compared to preoperative baseline (positive = improvement) |
| percentile |
Clip the limit to this percentile of the values (100 = no clipping), so one o… |
| period |
Sampling period for monitors (ms) |
| permutations |
Name of the observer parameter holding the fixed (n_perm, n) permutation-… |
| permute |
The symbol whose entries are permuted (the observation source, or a parameter… |
| pipeline |
Ordered sequence of Functions |
| placeholder |
Honest-placeholder text drawn when this panel’s data is missing or degenerate… |
| platform |
OS / architecture (e |
| position |
Spatial coordinates (x, y, z) of the node |
| post_expression |
Post-processing expression applied after coupling |
| pre_expression |
Pre-processing expression applied before coupling |
| precision |
Floating point precision: ‘float32’ or ‘float64’ |
| preconditioner |
|
| predicted |
Observation(s) the model PREDICTS, recomputed for every proposed theta |
| preprocessing |
Optional preprocessing to apply after loading |
| primary_weight |
Name of the edge group that should serve as the canonical weights matrix when… |
| priors |
Priors over the inferred parameters, keyed by each parameter’s dotted name (e |
| procedure |
Optional symbolic procedure for derived generators (e |
| processing_pipeline |
Processing pipeline used to generate the tractography |
| produced_by |
The experiment or analysis that computed it, by IRI (tvbo:exp/<study>/exp-<... | | [producer](slots/producer.qmd) | HOW to compute this value, when it is derived rather than obtained — the call... | | [programming_language](slots/programming_language.qmd) | Implementation languages | | [projection](slots/projection.qmd) | Which plane the region centres flatten onto | | [protocols](slots/protocols.qmd) | All DBS protocols assigned to this subject | | [provenance](slots/provenance.qmd) | W3C PROV-O aligned provenance for this entity — what it was derived from, whi... | | [pulse_width](slots/pulse_width.qmd) | | | [pycode](slots/pycode.qmd) | Python code for the equation | | [quantity_kind](slots/quantity_kind.qmd) | Scalar, vector, or tensor | | [query](slots/query.qmd) | BIDS entity filter that selects one per-subject file under the experiment's `... | | [queue](slots/queue.qmd) | Scheduler queue for the executor (Nextflow process | | [ramp](slots/ramp.qmd) | For method=from_working_point: the parameter + domain to ramp quasi-staticall... | | [random_seed](slots/random_seed.qmd) | Experiment-global RNG seed (default 0) | | [random_state](slots/random_state.qmd) | | | [recon_path](slots/recon_path.qmd) | | | [reconcile](slots/reconcile.qmd) | Align the sourced array's nodes to the consuming network by label (by_label… |
| reconstruction |
BIDS rec- entity (e |
| record |
Whether to include this element in simulation output files |
| reduce |
Opt into streaming evaluation of this observation: fold it into the integrato… |
| ref |
Git branch, tag, or commit to check out (git sources only) |
| reference |
DOI or citation for this dataset |
| reference_image |
The published figure this one reproduces, as a path relative to the study roo… |
| reference_publication |
DOI of the primary reference publication for this tool |
| references |
|
| region |
Brain region or anatomical label |
| region_mapping |
For hierarchical coupling: vertex-to-region mapping for aggregation |
| regional_connectivity |
For hierarchical coupling: region-to-region connectivity with weights and del… |
| regions |
Rectangles ringing the windows this panel calls out — the parameter band a re… |
| rel_tol |
Relative tolerance for ODE integration |
| relatedUBERONTerm |
Add the related anatomical entity as defined by the UBERON ontology |
| render |
Name of a registered custom-panel callable fn(container, ax, **opts) (custom … |
| replaces |
Dotted references to the post-scan pipeline reducers this streams |
| reported_optimum |
|
| repository |
Source code repository URL |
| required |
Whether a value for this parameter must be supplied |
| requirements |
|
| requires |
Observables required by this update rule |
| reset_state |
Start this stage from the model’s declared initial conditions rather than the… |
| results |
The named numbers the prose cites, each keyed by the manuscript token that st… |
| resync |
Recurrence rebuilding the state exactly from the whole window x |
| resync_masked |
Recurrence rebuilding the state from a fixed-size ring in which only L rows… |
| retries |
Automatic retries per failed task |
| rhs |
|
| right |
Strip reserved at the right — what cells carrying their ticks on that side ne… |
| rng |
Random-seed policy across shards |
| role |
Semantic key this directory is resolved by |
| rotation |
Text rotation in degrees counter-clockwise; 90 for a label running up the sid… |
| row_label_rotation |
Rotation of the row headings, in degrees |
| row_labels |
One heading per row, in the reserved left strip |
| rules |
Straight reference lines drawn across the panel: a zero, a threshold, the ide… |
| run_id |
BIDS run number |
| runtime_platform |
Execution backends or platforms (e |
| same_as |
URIs that unambiguously identify this tool (Wikidata, bio |
| sample |
|
| sampler |
MCMC sampler (‘nuts’) |
| sampling_period |
Time between samples (inverse of sampling_rate) |
| sampling_period_unit |
Unit of the sampling period (e |
| sampling_rate |
Sample rate of the dataLocation waveform in samples per millisecond (e |
| scale |
The scale this score belongs to, if applicable |
| scipy_ode_base |
|
| score |
|
| seed |
Random seed for reproducible graph generation |
| seed_offset |
Sub-stream this step draws from, offset from the generator’s seed |
| segmentation |
BIDS seg- entity (e |
| sel |
SLICE: label-based selector (xarray | | [sequential](slots/sequential.qmd) | Ordered magnitudes with no meaningful zero | | [session_id](slots/session_id.qmd) | BIDS session identifier | | [sessions](slots/sessions.qmd) | Data collection sessions for this subject | | [settings](slots/settings.qmd) | | | [settle_seed](slots/settle_seed.qmd) | Seed for the noise the settle integrates, when the settle runs as its own sca... | | [setup](slots/setup.qmd) | Shell lines run verbatim before the task command, afterset -euo pipefail... | | [sex](slots/sex.qmd) | Biological sex | | [shape](slots/shape.qmd) | Matrix dimensions [N, M] | | [share_x](slots/share_x.qmd) | Panel groups that share one x scale, each entry a comma-separated list of mos... | | [share_y](slots/share_y.qmd) | Panel groups that share one y scale, each entry a comma-separated list of mos... | | [show](slots/show.qmd) | Whether the bar is drawn | | [sigma](slots/sigma.qmd) | Observation-noise scale of the likelihood | | [simulation_experiments](slots/simulation_experiments.qmd) | | | [simulation_period](slots/simulation_period.qmd) | Duration of each simulation step (e | | [size](slots/size.qmd) | Text size in points, overriding the figure's font size for this label alone | | [slurm](slots/slurm.qmd) | Slurm sbatch directives for array-job execution | | [snakemake](slots/snakemake.qmd) | Snakemake execution directives | | [software](slots/software.qmd) | | | [software_environment](slots/software_environment.qmd) | Software environment used to generate this data | | [solver](slots/solver.qmd) | ODE solver for time_integration method | | [source](slots/source.qmd) | | | [source_branch](slots/source_branch.qmd) | Name of a previously computed branch (for from_branch method) | | [source_code](slots/source_code.qmd) | | | [source_experiment](slots/source_experiment.qmd) | For method=from_experiment: the experiment whose settled per-node endpoint st... | | [source_network](slots/source_network.qmd) | Path or name of the Network whose nodes define the source endpoints of this E... | | [source_point](slots/source_point.qmd) | Which point of the source branch/run seeds this run: 'endpoint' (default, the... | | [source_url](slots/source_url.qmd) | Canonical source or repository URL | | [source_var](slots/source_var.qmd) | Output variable from source node to use (e | | [sources](slots/sources.qmd) | | | [space](slots/space.qmd) | Exploration axes spanning the search space, keyed by the dotted parameter ref... | | [sparse](slots/sparse.qmd) | Whether the coupling uses sparse representations | | [spine_offset](slots/spine_offset.qmd) | How far the left and bottom spines sit outside the data area, in axes fractio... | | [spines](slots/spines.qmd) | Axes spine style: 'box' (all 4 spines, closed boxes — e | | [stages](slots/stages.qmd) | Ordered list of optimization stages | | [started_at](slots/started_at.qmd) | ISO 8601 start time | | [state](slots/state.qmd) | Per-node initial state variable values, keyed by state variable name | | [state_variables](slots/state_variables.qmd) | | | [state_wise_sigma](slots/state_wise_sigma.qmd) | | | [statistic](slots/statistic.qmd) | Statistic used to collapse the axis (mean, sum, std, sem, median) | | [step](slots/step.qmd) | Step size | | [step_size](slots/step_size.qmd) | Fixed time step of the solver | | [steps](slots/steps.qmd) | Ordered intermediate steps, keyed by name — the same keyed-collection form as... | | [still](slots/still.qmd) | Which frame is also saved as a still image beside the movie, for the contexts... | | [stimulation](slots/stimulation.qmd) | | | [stimulation_variable](slots/stimulation_variable.qmd) | | | [stimulus](slots/stimulus.qmd) | | | [strategy](slots/strategy.qmd) | Search strategy over the decision space (the `space` axes) | | [structural_measures](slots/structural_measures.qmd) | BEP017 measure names for structural connectivity (e | | [studies](slots/studies.qmd) | Other studies this one aggregates, each aSimulationStudyin its own righ... | | [style](slots/style.qmd) | Style layers underneath the theme, applied left to right: a registered bsplot... | | [subdir](slots/subdir.qmd) | Subdirectory within the source to place on the import path (defaults to the s... | | [subdirs](slots/subdirs.qmd) | Directories under the dataset root, in the order a reader should meet them | | [subject_id](slots/subject_id.qmd) | BIDS subject identifier | | [subjects](slots/subjects.qmd) | Ordered list of subject IDs (e | | [subnetwork](slots/subnetwork.qmd) | Optional finer-scale Network that "lives inside" this Node (network-of-networ... | | [suffix](slots/suffix.qmd) | BIDS suffix (e | | [surface](slots/surface.qmd) | Geometry and colour scale of a `kind: surface` panel | | [surface_atlas](slots/surface_atlas.qmd) | The atlas to read vertex labels from, where it differs from the one the value... | | [surrogate](slots/surrogate.qmd) | Optional permutation-significance test: this derived variable's value is the ... | | [sweep_direction](slots/sweep_direction.qmd) | Order in which a branch-following axis (sweep_seeding: from_previous) is trav... | | [sweep_seeding](slots/sweep_seeding.qmd) | How each sweep point's initial state is obtained | | [symbol](slots/symbol.qmd) | | | [symmetric](slots/symmetric.qmd) | Centre the limits on zero, so zero is the map's midpoint | | [symmetry](slots/symmetry.qmd) | Edge symmetry type for NetworkDynamics | | [system_size](slots/system_size.qmd) | System size (van Kampen Ω) for the stochastic 'gillespie' backend: the number... | | [system_type](slots/system_type.qmd) | | | [tail](slots/tail.qmd) | | | [tail_duration](slots/tail_duration.qmd) | Length of the trailing window as a duration, in the same time unit as the int... | | [tail_samples](slots/tail_samples.qmd) | Number of samples from the end to use | | [tail_used](slots/tail_used.qmd) | The arrow tail's y, read from a result container (same reference form a Layer... | | [tail_x](slots/tail_x.qmd) | Start the arrow at this x in DATA coordinates instead of at an axes-fraction ... | | [target](slots/target.qmd) | Target node ID (set for explicit edges, absent for template edges) | | [target_component](slots/target_component.qmd) | Component to attach this event to | | [target_data](slots/target_data.qmd) | Reference to empirical data observation for matching objectives | | [target_network](slots/target_network.qmd) | Path or name of the Network whose nodes define the target endpoints (e | | [target_parameter](slots/target_parameter.qmd) | The parameter to update (e | | [target_range](slots/target_range.qmd) | Target interval for a `minmax_rescale` step (e | | [target_regions](slots/target_regions.qmd) | Regions a stimulus-type event targets: 'all' (broadcast to every node) or exp... | | [target_structure](slots/target_structure.qmd) | Anatomical target structure from a brain atlas | | [target_value](slots/target_value.qmd) | Target value for activity objectives | | [target_var](slots/target_var.qmd) | Input variable on target node to connect to (e | | [target_variable](slots/target_variable.qmd) | State variable that a stimulus-type event drives — the variable its signal is... | | [targets](slots/targets.qmd) | State variables this noise applies to; if omitted, applies globally | | [task_iri](slots/task_iri.qmd) | Cognitive Atlas (cogat:) IRI of the assessment instrument / task that pro... | | [task_name](slots/task_name.qmd) | BIDS task name for the simulation (e | | [template](slots/template.qmd) | Asset that seeds the file attvbo study init, resolved against the scaffo... | | [template_variants](slots/template_variants.qmd) | Seeds that supersedetemplatefor one init variant, keyed by variant name | | [templates](slots/templates.qmd) | The kinds of study this record covers, keyed by the nametvbo study init –… |
| tensor_coefficient |
Optional anisotropic tensor (e |
| terminology |
Add the parcellation terminology version used for this brain atlas version |
| text |
The label |
| theme |
The look this figure declares: its colours and the geometry a style sheet use… |
| threshold_applied |
Threshold value applied to the E-field simulation |
| tick_direction |
Whether tick marks point out of the axes, into them, or both |
| tick_length |
Length of this panel’s tick marks in points, overriding the theme’s |
| tick_pad |
Distance from a tick mark to its label, in points |
| tick_prune |
Drop the first, last, or both end ticks, for the case where a corner tick col… |
| tick_size |
Tick-label size in points, overriding the figure’s font_size for this panel… |
| tick_width |
Line weight of a major tick mark, in points |
| ticklabels |
Text for the marked values of a STANDALONE kind: colorbar panel, where the … |
| ticks |
The values to mark |
| time |
Wall-clock limit per task (e |
| time_dependent |
|
| time_post_surgery |
Timepoint of assessment in days or months after implantation |
| time_range |
Time range for generated TimeSeries (for kernel generators) |
| time_unit |
Unit of every time-valued number in this scope — the step size, any period, a… |
| timepoint |
Timepoint of assessment (e |
| timing_info |
|
| title |
A heading above the panel, in the panel’s own words |
| title_pad |
Distance from a panel title to the axes, in points |
| tol_stability |
Tolerance on real part of eigenvalue for stability boundary |
| tool_role |
Primary function(s) in a simulation workflow |
| top |
Strip reserved at the top for the column labels |
| traceable |
Whether this callable can be traced by an array-programming backend (jit/vmap… |
| tracked |
What version control keeps, which is what the | | [tractogram](slots/tractogram.qmd) | Reference to tractography data | | [trailing](slots/trailing.qmd) | Text written after the last cell, closing such an equation | | [trajectory](slots/trajectory.qmd) | The planned trajectory for electrode implantation | | [transform](slots/transform.qmd) | Optional named reduction applied to the sourced array aftersel, before `... | | [transforms](slots/transforms.qmd) | Ordered list of transforms applied to edge property matrices | | [transient_time](slots/transient_time.qmd) | Length of the leading settling window, prepended to `duration` | | [triangle](slots/triangle.qmd) | Fill only this triangle of a square matrix, masking the other half so a sibli... | | [triangle_gap](slots/triangle_gap.qmd) | Cells of blank left along the diagonal between two `triangle` layers, so the ... | | [trigger_times](slots/trigger_times.qmd) | Predetermined trigger times for preset_time events | | [trim_margins](slots/trim_margins.qmd) | Trim surrounding whitespace from the saved figure (default true) | | [truncation_window](slots/truncation_window.qmd) | Truncated-BPTT window in milliseconds of simulated time: gradients flow back ... | | [type](slots/type.qmd) | Controlled-vocabulary terms narrowing what kind of activity this was | | [unit](slots/unit.qmd) | Physical unit of measurement | | [units](slots/units.qmd) | How this tool spells the units TVBO declares | | [update_expression](slots/update_expression.qmd) | | | [update_rules](slots/update_rules.qmd) | How parameters are updated each iteration | | [url](slots/url.qmd) | (Deprecated) Use source_url | | [used](slots/used.qmd) | | | [va](slots/va.qmd) | Vertical alignment against (x, y) — bottom, center, top, baseline | | [valid_diagonal](slots/valid_diagonal.qmd) | Self-connections are meaningful | | [value](slots/value.qmd) | Numeric, string, or boolean value, OR an array (nested list) for array-valued... | | [values](slots/values.qmd) | | | [variable_of_interest](slots/variable_of_interest.qmd) | | | [variant](slots/variant.qmd) | Thetvbo study init –template`name this seed belongs to | | [vectorize](slots/vectorize.qmd) | Axis names or parameters to pack into a single vectorized backend call | | [vectorized](slots/vectorized.qmd) | Opt in to the vectorized matmul fast path for a source-only coupling — one wh... | | [venv](slots/venv.qmd) | Path to a virtual environment to activate before running | | [version](slots/version.qmd) | Version of the instrument (e | | [version_spec](slots/version_spec.qmd) | Version or constraint specifier (e | | [vertex_to_region](slots/vertex_to_region.qmd) | Array mapping each vertex index to its parent region index | | [vertices_field](slots/vertices_field.qmd) | When the mesh is inlined on a Network, the dotted path inside the parent's h5... | | [view](slots/view.qmd) | Where the camera sits | | [vmax](slots/vmax.qmd) | The value the scale ends at | | [vmin](slots/vmin.qmd) | The value the scale starts at | | [voi](slots/voi.qmd) | Variable of interest index (which state variable to monitor) | | [volume](slots/volume.qmd) | Geometry and colour scale of akind: volumepanel | | [volume_data](slots/volume_data.qmd) | Reference to raw or thresholded volume | | [wait_selector](slots/wait_selector.qmd) | CSS selector to wait for before capturing, so the shot is taken only once the... | | [warmup](slots/warmup.qmd) | Extra settle time in seconds after load / wait_selector, for late layout or a... | | [warmup_from](slots/warmup_from.qmd) | Previous stage to initialize from | | [waves](slots/waves.qmd) | Per-group boolean derived variable: a wave is present this timestep | | [weight](slots/weight.qmd) | Connection weight (explicit edges) | | [weight_distribution](slots/weight_distribution.qmd) | Distribution to sample per-region stimulus weights from, as an alternative to... | | [weight_parameter](slots/weight_parameter.qmd) | Per-node stimulus weighting supplied as a Parameter, so a DERIVED weighting c... | | [weighted](slots/weighted.qmd) | Matrix entries carry weights (not just 0/1) | | [weighting](slots/weighting.qmd) | | | [weights](slots/weights.qmd) | Per-node stimulus weighting, aligned withnodes| | [width](slots/width.qmd) | Figure width in mm (physical print size) | | [width_ratios](slots/width_ratios.qmd) | Relative widths of the mosaic columns | | [window_size](slots/window_size.qmd) | Number of samples for windowed aggregation | | [workflow](slots/workflow.qmd) | Axis names or parameters to fan out into independent scheduler tasks (one wor... | | [workflow_overrides](slots/workflow_overrides.qmd) | Per-figure HPC/workflow resource refinement (reuses WorkflowConfig, same patt... | | [wrt](slots/wrt.qmd) | Quantity/quantities the analysis is taken with respect to, e | | [wspace](slots/wspace.qmd) | Gap between columns, as a fraction of the panel | | [x](slots/x.qmd) | X coordinate | | [xlabel](slots/xlabel.qmd) | The x axis label, as the figure prints it — unit included, LaTeX included | | [xlabel_pad](slots/xlabel_pad.qmd) | Gap in points between the x axis label and its tick numbers, for where the de... | | [xlabel_side](slots/xlabel_side.qmd) | Which edge the x axis LABEL sits on | | [xlim](slots/xlim.qmd) | The x range,[min, max]| | [xscale](slots/xscale.qmd) | How the x axis maps values to distance | | [xtick_format](slots/xtick_format.qmd) | How x tick numbers are written:sciforces scientific notation,plainfor... | | [xtick_rotation](slots/xtick_rotation.qmd) | Rotate the x tick labels, in degrees counter-clockwise | | [xtick_side](slots/xtick_side.qmd) | Which edge the x ticks sit on | | [xticks](slots/xticks.qmd) | The x tick positions, stated outright | | [y](slots/y.qmd) | Y coordinate | | [year](slots/year.qmd) | | | [ylabel](slots/ylabel.qmd) | The y axis label | | [ylabel_pad](slots/ylabel_pad.qmd) | Gap in points between the y axis label and its tick numbers | | [ylabel_side](slots/ylabel_side.qmd) | Which edge the y axis LABEL sits on | | [ylim](slots/ylim.qmd) | The y range,[min, max]| | [yscale](slots/yscale.qmd) | How the y axis maps values to distance | | [ytick_format](slots/ytick_format.qmd) | How y tick numbers are written | | [ytick_rotation](slots/ytick_rotation.qmd) | Rotate the y tick labels, in degrees counter-clockwise | | [ytick_side](slots/ytick_side.qmd) | Which edge the y ticks sit on | | [yticks](slots/yticks.qmd) | The y tick positions, stated outright | | [z](slots/z.qmd) | Z coordinate | | [zlabel](slots/zlabel.qmd) | The depth axis label of a 3-D panel | | [zlabel_pad](slots/zlabel_pad.qmd) | Gap in points between the z axis label and its tick numbers | | [zlim](slots/zlim.qmd) | The depth range of a 3-D panel,[min, max]` |
| zoom |
Scale factor on the projected view; above 1 moves the camera in |