Get started:

  • Get Arbor
    • Python Installation
      • Getting Arbor
        • Customising Arbor
        • Advanced options
      • Note on performance
    • Spack Installation
      • Install Arbor
      • Build Options
      • Why use Spack?
      • Issues when using Spack
    • Build and install from source
      • Getting the code
      • Requirements
        • Dependencies
        • Minimum requirements
        • Optional requirements
      • Building and installing Arbor
        • Quick start: examples
        • Build target
        • Architecture
        • Vectorization
        • GPU backend
        • Python frontend
        • NeuroML support
        • Profiling
        • Installation
      • HPC clusters
        • MPI
        • Heterogeneous systems
        • Cray systems
      • Troubleshooting
        • Cross compiling NMODL
        • Debugging
        • CMake Git submodule warnings
  • Tutorials
    • Cells
      • A simple single cell model
        • The cell
        • The single cell model
        • The results
        • The full code
      • Single Cell in GUI
        • Get the GUI
        • Define a Morphology
        • Defining Locations
        • Assigning Bio-physical Properties
        • Setting up the Simulation
        • Running Simulations and Getting Outputs
        • Where to go from here
      • A detailed single cell model
        • The cell
        • The model
        • The full code
      • A simple dendrite
        • The full code
        • Walk-through
      • A single cell model from the Allen Brain Atlas
        • Obtaining the model
        • The morphology
        • The parameter fit
        • The decor
        • The model
        • The result
        • The full code
      • A single cell model from the BluePyOpt Cell Optimisation Library
        • The model
        • Export to JSON/ACC
        • Load from JSON/ACC
        • Axon replacement
        • Define locations in the GUI
        • The cable cell and protocols
        • Running the simulation
        • The full code
    • Recipes
      • A simple single cell recipe
        • The cell
        • The recipe
        • The simulation
        • The results
      • A detailed single cell recipe
        • The cell
        • The recipe
        • The simulation
        • The results
        • The full code
    • Networks
      • A ring network
        • The cell
        • The recipe
        • The execution
        • The results
        • The full code
      • Two cells connected via a gap junction
        • Walk-through
        • The full code
    • Probes
      • Extracellular signals (LFPykit)
        • The line source approximation
        • The model
        • Compute extracellular potentials
        • The result
        • The full code
        • References
    • Stochastic Mechanisms
      • Spike Timing-dependent Plasticity Curve
        • Implementation of a Stochastic Mechanism
        • The Model
        • The full code
        • References
    • Hardware
      • Distributed ring network (MPI)
        • The recipe
        • The hardware context
        • The execution
        • The results
        • The full code
      • GPU and profiling
        • The hardware context
        • Profiling
        • The domain decomposition
        • The simulation
        • The execution
        • The results
        • The full code
    • Demonstrations
  • Ecosystem
    • Arbor models
    • Arbor software
    • Wider ecosystem
      • Simulators
      • Frameworks
  • Contributing
    • Howtos
      • File an Issue
      • Make a Pull Request
        • Issues
        • Making a pull request
        • Collaborating on a PR
        • Reviewing a PR
        • Merging a PR
      • Share a model
      • Write code
        • Python
        • C++
        • Code organisation
        • Namespaces
        • Formatting statements
        • Memory management
        • Header files
      • Modify documentation
        • Tutorials
        • Update policy
        • Labels and filename conventions
        • Language
      • Add examples
        • Tutorials
      • Add test
        • What to test?
        • C++ tests
        • Python tests
        • Feature dependent tests
      • Make a release
        • Release cycle
        • Procedure
        • GUI
      • Dependency management
        • List of dependencies
        • User platforms
        • Dependency update rules
    • Code of Conduct
      • Concerns
      • Ebrains

Concepts:

  • Concepts overview
  • Recipes
    • An example model
    • Are recipes always necessary?
    • Why recipes?
    • General best practices
    • API
  • Cells
    • Cell kind
    • Cell description
    • API
  • Interconnectivity
    • API
  • Hardware context
    • Execution context
    • API
  • Domain decomposition
    • Load balancers
    • API
  • Simulations
    • From recipe to simulation
    • Configuring data extraction
    • Simulation execution and interaction
    • API
  • Cable cells
    • Cable cell morphology
      • Segment trees
      • Morphology
        • Examples
      • Editing morphologies
      • Supported file formats
      • Discretisation and CV policies
        • Composition of CV policies
        • Reading CV policies from strings
      • API
    • Cable cell labels
      • Example cell
      • Label types
      • Expressions
        • Expression syntax
        • Locset expressions
        • Region expressions
        • Inhomogeneous Expressions
      • Thingification
        • Locations
        • Cables
      • Label Dictionaries
      • API
    • Cable cell mechanisms
      • Mechanism catalogues
        • Built-in Catalogues
        • Adding Catalogues to Arbor
        • Parameters
      • Mechanism types
        • Density mechanisms
        • Ion reversal potential mechanisms
        • Point mechanisms
        • Junction mechanisms
        • Stochastic Processes
      • API
    • Cable cell decoration
      • Painted dynamics
        • 1. Cable properties
        • 3. Density mechanisms
        • 4. Scaled mechanisms
        • 5. Ion species
      • Placed dynamics
        • 1. Connection sites
        • 2. Threshold detectors.
        • 3. Gap junction connection sites
        • 4. Stimuli
        • 5. Probes
      • API
    • API
  • LIF cells
    • API
  • Spike source cells
    • API
  • Benchmark cells
    • API
  • Probing and Sampling
    • Definitions
    • Spiking
      • API

Modelling:

  • Modelling

File formats:

  • SWC
    • Arbor interpretation
    • NEURON interpretation
    • API
  • NeuroML2
    • Example
    • API
  • Neurolucida ASCII
    • Soma / CellBody
    • API
  • NMODL
    • Units
    • Ions
    • Special variables
    • Functions, procedures and blocks
    • Unsupported features
    • Arbor-specific features
    • Voltage Processes
    • Stochastic Processes
    • Nernst
    • Tips for Faster NMODL
      • RANGE
      • PROCEDURE
      • PARAMETER
      • Sharing Expressions Between INITIAL and BREAKPOINT or DERIVATIVE
      • Complex Expressions in Current Computation
      • Using Memory versus Computation
      • Specialised Functions
      • Small Tips and Micro-Optimisations
  • Arbor Cable Cell
    • Label dictionary
    • Decor
    • Morphology
    • Cable cell
    • Parsable arbor-components and meta-data
      • Label-dict
      • Decoration
      • Morphology
      • Cable-cell
    • API

API reference:

  • Python
    • Recipes
      • Recipe
        • recipe
      • Cells
      • Synapses
      • Event generator and schedules
        • event_generator
        • regular_schedule
        • explicit_schedule
        • poisson_schedule
      • Example
    • Cells
      • Cell identifiers and indexes
        • selection_policy
        • cell_local_label
        • cell_global_label
        • cell_member
        • cell_kind
      • Cell kinds
    • Interconnectivity
      • connection
        • connection.connection()
        • connection.source
        • connection.dest
        • connection.weight
        • connection.delay
      • gap_junction_connection
        • gap_junction_connection.peer
        • gap_junction_connection.local
        • gap_junction_connection.weight
      • threshold_detector
        • threshold_detector.threshold
    • Hardware context
      • Available resources
        • config()
        • mpi_init()
        • mpi_is_initialized()
        • mpi_comm
        • mpi_finalize()
        • mpi_is_finalized()
      • Env: Helper functions
        • find_private_gpu()
      • Prescribed resources
        • proc_allocation
        • context
    • Domain decomposition
      • Load balancers
        • partition_load_balance()
        • partition_by_group()
        • partition_hint
      • Decomposition
        • backend
        • domain_decomposition
        • group_description
    • Simulations
      • From recipe to simulation
        • simulation
        • binning
        • spike_recording
        • sampling_policy
      • Recording spikes
      • Recording samples
        • Procedure
        • Example
    • Profiler
    • Meter manager
      • Marking metering regions
        • meter_manager
      • Metering output
        • meter_report
    • Cable cells
      • Cable cell morphology
        • mnpos
        • location
        • cable
        • mpoint
        • segment
        • segment_tree
        • morphology
        • place_pwlin
        • isometry
        • Discretisation and CV policies
        • CV discretization as mcables
        • SWC
        • NeuroML
        • Neurolucida
      • Cable cell labels
        • label_dict
      • Cable cell mechanisms
        • mechanism
        • density
        • synapse
        • junction
        • mechanism_info
        • ion_dependency
        • mechanism_field
        • Mechanism catalogues
      • Cable cell decoration
        • decor
      • Cable cell probing and sampling
        • Example
        • API
      • LIF Cell probing
        • lif_probe_voltage()
      • Description Format
        • The arbor-components and meta-data
        • Reading and writing arbor-components
      • cable_cell
        • cable_cell.__init__()
        • cable_cell.placed_lid_range()
      • ion
      • cable_cell_global_properties
        • cable_cell_global_properties.catalogue
        • cable_cell_global_properties.membrane_voltage_limit
        • cable_cell_global_properties.ion_data
        • cable_cell_global_properties.ion_valence
        • cable_cell_global_properties.ion_reversal_potential
        • cable_cell_global_properties.ions
        • cable_cell_global_properties.unset_ion()
        • cable_cell_global_properties.membrane_potential
        • cable_cell_global_properties.membrane_capacitance
        • cable_cell_global_properties.temperature
        • cable_cell_global_properties.axial_resisitivity
    • LIF cells
      • lif_cell
        • lif_cell.lif_cell()
        • lif_cell.source
        • lif_cell.target
        • lif_cell.tau_m
        • lif_cell.V_th
        • lif_cell.C_m
        • lif_cell.E_L
        • lif_cell.E_R
        • lif_cell.V_m
        • lif_cell.t_ref
    • Spike source cells
      • spike_source_cell
        • spike_source_cell.spike_source_cell()
    • Benchmark cells
      • benchmark_cell
        • benchmark_cell.benchmark_cell()
    • Single cell model
      • single_cell_model
        • single_cell_model.single_cell_model()
        • single_cell_model.run()
        • single_cell_model.probe()
        • single_cell_model.spikes()
        • single_cell_model.traces()
        • single_cell_model.properties
        • single_cell_model.catalogue
      • trace
        • trace.variable
        • trace.loc
        • trace.t
        • trace.v
  • C++
    • Recipes
      • C++ best practices
      • Recipe
      • Cells
      • Synapses
      • Probes
      • Event generator and schedules
      • Example
    • Cells
      • Cell identifiers and indexes
    • Interconnectivity
    • Hardware context
      • libarborenv
      • libarbor
      • Distributed context
        • Class documentation
      • Dry-run mode
    • Domain decomposition
      • Decomposition
      • Load balancers
    • Simulations
      • From recipe to simulation
      • Class documentation
    • Profiler
      • Compilation
      • Instrumenting code
        • Marking regions
        • Organising regions
      • Running the profiler
        • Profiler output
    • Cable cells
      • Cable cell morphology
        • Segment tree
        • Morphology API
        • Identifying sites and subsets of the morphology
        • Translating regions and locsets to cables and locations
        • From morphologies to points and segments
        • Discretisation and CV policies
        • CV discretization as mcables
      • Supported morphology formats
        • SWC
        • Neurolucida ASCII
        • NeuroML
      • Cable cell probing and sampling
        • Cable cell probes
        • Sampling API
      • LIF cell probing and sampling
        • Membrane voltage
      • Description Format
        • The arbor-components and meta-data
        • Reading arbor-components
        • Writing arbor-components
      • The cable_cell object
      • Cell dynamics
      • Electrical properties and ion values
      • Global properties
      • Reversal potential dynamics
      • Overriding properties locally
    • LIF cells
  • Developers Guide
    • How the Cable Cell is made
      • Terminology
      • Setting up a Cable Cell simulation
      • Lowered Cells, Shared State, and the Discretisation
      • Main integration loop
    • Cell groups
      • Cable Cell group mc_cell_group
    • Communication in Arbor
    • Exchange of Spikes
    • Distribution of Events to Targets
    • Building the Connection Table
    • Debugging
      • Backtraces
    • Matrix Solvers
      • Cable Equation
      • CPU
        • Assembly
        • Solving
      • GPU
    • Stochastic Differential Equations
      • Analytical Solutions
      • Euler-Maruyama Solver
      • Stochastic Mechanisms
      • Random Number Generation
      • Normal Distribution
    • SIMD Classes
      • Classes
        • Indirect expressions
        • Class simd
        • Class simd_mask
        • Class where_expression
      • Top-level functions
      • Implementation requirements
        • Minimal implementation
        • Concrete implementation API
      • Missing functionality
      • Implementation of vector transcendental functions
        • Exponentials
        • Logarithms
    • Shared State
      • Ions
      • Mechanisms
      • Further Functionality
    • Exporting Symbols
      • Macro Description
    • Adding Built-in Catalogues to Arbor
    • Mechanism ABI
      • Metadata: arb_mechanism_type
        • Tables
      • Interlude: Parameter packs
        • User Data
      • Implementation: arb_mechanism_interface
      • SIMDization
      • Making A Loadable Mechanism
      • Writing Mechanisms Directly Against the ABI
    • Utility wrappers and containers
    • Version and build information
      • Version information
      • Source information
      • Build information
      • Features
      • Full build information
    • Numerical methods
      • Passive cable
      • Mechanisms
Arbor v: latest
Arbor
  • Docs  » 
  • File formats

File formats¶

Name

File extension

Read

Write

Arbor Cable Cell

acc

✓

✓

SWC

swc

✓

✗

NMODL

mod

✓

✗

NeuroML2

nml

✓

✗

Neurolucida

asc

✓

✗

  • Arbor Cable Cell
    • Label dictionary
    • Decor
    • Morphology
    • Cable cell
    • Parsable arbor-components and meta-data
    • API
  • Neurolucida ASCII
    • Soma / CellBody
    • API
  • NeuroML2
    • Example
    • API
  • NMODL
    • Units
    • Ions
    • Special variables
    • Functions, procedures and blocks
    • Unsupported features
    • Arbor-specific features
    • Voltage Processes
    • Stochastic Processes
    • Nernst
    • Tips for Faster NMODL
  • SWC
    • Arbor interpretation
    • NEURON interpretation
    • API

© Copyright 2017-2022, ETHZ & FZJ. Revision feb4d148.

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