Blue Brain BioExplorer
Classes | Typedefs | Enumerations | Variables
bioexplorer::morphology Namespace Reference

Classes

struct  Synapse
 
struct  AstrocyteSoma
 
struct  NeuronSoma
 
struct  Section
 
struct  EndFoot
 
struct  Cell
 
class  Astrocytes
 
class  AstrocytesLoader
 
class  CompartmentSimulationHandler
 The CompartmentSimulationHandler handles the reading of simulation information from the database at a compartment level. When attached to a model, the simulation data is communicated to the renderer by Core, and mapped to the geometry by the BioExplorer advanced renderer. More...
 
class  Morphologies
 The Morphologies class. More...
 
class  Neurons
 
class  NeuronsLoader
 
class  SomaSimulationHandler
 The SomaSimulationHandler handles the reading of simulation information from the database at a soma level. When attached to a model, the simulation data is communicated to the renderer by Core, and mapped to the geometry by the BioExplorer advanced renderer. More...
 
class  SpikeSimulationHandler
 The SpikeSimulationHandler handles the reading of simulation information from the database at a soma level. When attached to a model, the simulation data is communicated to the renderer by Core, and mapped to the geometry by the BioExplorer advanced renderer. More...
 
class  Synapses
 

Typedefs

using MorphologiesPtr = std::shared_ptr< Morphologies >
 
using AstrocytesPtr = std::shared_ptr< Astrocytes >
 
using NeuronsPtr = std::shared_ptr< Neurons >
 
using SynapsesPtr = std::shared_ptr< Synapses >
 
using SynapsesMap = std::map< uint64_t, Synapse >
 
using SegmentSynapseMap = std::map< uint64_t, std::vector< Synapse > >
 
using SectionSynapseMap = std::map< uint64_t, SegmentSynapseMap >
 
using AstrocyteSomaMap = std::map< uint64_t, AstrocyteSoma >
 
using NeuronSomaMap = std::map< uint64_t, NeuronSoma >
 
using SectionMap = std::map< uint64_t, Section >
 
using EndFootMap = std::map< uint64_t, EndFoot >
 
using CellMap = std::map< uint64_t, Cell >
 
using SpikesMap = std::map< uint64_t, float >
 
using Varicosities = std::map< uint64_t, Vector3ds >
 

Enumerations

enum class  MorphologySynapseType {
  none = 0 , afferent = 1 , efferent = 2 , debug = 4 ,
  all = 8
}
 
enum class  PopulationColorScheme { none = 0 , id = 1 }
 
enum class  MorphologyColorScheme { none = 0 , section_type = 1 , section_orientation = 2 , distance_to_soma = 3 }
 
enum class  MorphologyRepresentation {
  graph = 0 , section = 1 , segment = 2 , orientation = 3 ,
  bezier = 4 , contour = 5 , surface = 6
}
 
enum class  MorphologyRealismLevel {
  none = 0 , soma = 1 , axon = 2 , dendrite = 4 ,
  internals = 8 , externals = 16 , spine = 32 , end_foot = 64 ,
  all = 255
}
 
enum class  MicroDomainRepresentation { mesh = 0 , convex_hull = 1 , surface = 2 }
 

Variables

const double mitochondrionSegmentSize = 0.25
 
const double mitochondrionRadius = 0.1
 
const double spineRadiusRatio = 0.5
 
const double myelinSteathLength = 10.0
 
const double myelinSteathRadiusRatio = 3.0
 
const uint64_t nbMinSegmentsForVaricosity = 10
 
const double DEFAULT_MITOCHONDRIA_DENSITY = 0.0459
 
const double DEFAULT_ENDFOOT_RADIUS_RATIO = 1.1
 
const double DEFAULT_ENDFOOT_RADIUS_SHIFTING_RATIO = 0.35
 
const std::string LOADER_NAME = LOADER_ASTROCYTES
 
const std::string SUPPORTED_PROTOCOL_ASTROCYTES = "astrocytes://"
 
const double DEFAULT_SPINE_RADIUS = 0.25
 
const size_t NB_MATERIALS_PER_MORPHOLOGY = 10
 
const size_t MATERIAL_OFFSET_VARICOSITY = 0
 
const size_t MATERIAL_OFFSET_SOMA = 1
 
const size_t MATERIAL_OFFSET_AXON = 2
 
const size_t MATERIAL_OFFSET_DENDRITE = 3
 
const size_t MATERIAL_OFFSET_APICAL_DENDRITE = 4
 
const size_t MATERIAL_OFFSET_AFFERENT_SYNAPSE = 5
 
const size_t MATERIAL_OFFSET_EFFERENT_SYNAPSE = 6
 
const size_t MATERIAL_OFFSET_MITOCHONDRION = 7
 
const size_t MATERIAL_OFFSET_NUCLEUS = 8
 
const size_t MATERIAL_OFFSET_MYELIN_SHEATH = 9
 
const size_t MATERIAL_OFFSET_END_FOOT = 4
 
const size_t MATERIAL_OFFSET_MICRO_DOMAIN = 5
 
const int64_t SOMA_AS_PARENT = -1
 
const uint64_t NB_MYELIN_FREE_SEGMENTS = 4
 
const double DEFAULT_ARROW_RADIUS_RATIO = 10.0
 
const uint64_t DEFAULT_DEBUG_SYNAPSE_DENSITY_RATIO = 5
 
const double MAX_SOMA_RADIUS = 10.0
 
std::map< ReportType, std::string > reportTypeAsString
 
const doubles MITOCHONDRIA_DENSITY = {0.0459, 0.0522, 0.064, 0.0774, 0.0575, 0.0403}
 
const std::string SUPPORTED_PROTOCOL_NEURONS = "neurons://"
 

Typedef Documentation

◆ AstrocyteSomaMap

using bioexplorer::morphology::AstrocyteSomaMap = typedef std::map<uint64_t, AstrocyteSoma>

Definition at line 366 of file Types.h.

◆ AstrocytesPtr

using bioexplorer::morphology::AstrocytesPtr = typedef std::shared_ptr<Astrocytes>

Definition at line 330 of file Types.h.

◆ CellMap

using bioexplorer::morphology::CellMap = typedef std::map<uint64_t, Cell>

Definition at line 406 of file Types.h.

◆ EndFootMap

using bioexplorer::morphology::EndFootMap = typedef std::map<uint64_t, EndFoot>

Definition at line 396 of file Types.h.

◆ MorphologiesPtr

using bioexplorer::morphology::MorphologiesPtr = typedef std::shared_ptr<Morphologies>

Definition at line 327 of file Types.h.

◆ NeuronSomaMap

using bioexplorer::morphology::NeuronSomaMap = typedef std::map<uint64_t, NeuronSoma>

Definition at line 377 of file Types.h.

◆ NeuronsPtr

using bioexplorer::morphology::NeuronsPtr = typedef std::shared_ptr<Neurons>

Definition at line 332 of file Types.h.

◆ SectionMap

using bioexplorer::morphology::SectionMap = typedef std::map<uint64_t, Section>

Definition at line 386 of file Types.h.

◆ SectionSynapseMap

using bioexplorer::morphology::SectionSynapseMap = typedef std::map<uint64_t, SegmentSynapseMap>

Definition at line 358 of file Types.h.

◆ SegmentSynapseMap

using bioexplorer::morphology::SegmentSynapseMap = typedef std::map<uint64_t, std::vector<Synapse> >

Definition at line 357 of file Types.h.

◆ SpikesMap

using bioexplorer::morphology::SpikesMap = typedef std::map<uint64_t, float>

Definition at line 468 of file Types.h.

◆ SynapsesMap

using bioexplorer::morphology::SynapsesMap = typedef std::map<uint64_t, Synapse>

Definition at line 356 of file Types.h.

◆ SynapsesPtr

using bioexplorer::morphology::SynapsesPtr = typedef std::shared_ptr<Synapses>

Definition at line 334 of file Types.h.

◆ Varicosities

using bioexplorer::morphology::Varicosities = typedef std::map<uint64_t, Vector3ds>

Definition at line 35 of file Neurons.h.

Enumeration Type Documentation

◆ MicroDomainRepresentation

enum bioexplorer::morphology::MicroDomainRepresentation
strong
Enumerator
mesh 
convex_hull 
surface 

Definition at line 462 of file Types.h.

◆ MorphologyColorScheme

enum bioexplorer::morphology::MorphologyColorScheme
strong
Enumerator
none 

All sections use the same color

section_type 

Colored by section

section_orientation 

section orientation

distance_to_soma 

distance to soma

Definition at line 426 of file Types.h.

◆ MorphologyRealismLevel

enum bioexplorer::morphology::MorphologyRealismLevel
strong
Enumerator
none 
soma 
axon 
dendrite 
internals 
externals 
spine 
end_foot 
all 

Definition at line 449 of file Types.h.

◆ MorphologyRepresentation

enum bioexplorer::morphology::MorphologyRepresentation
strong
Enumerator
graph 
section 
segment 
orientation 
bezier 
contour 
surface 

Definition at line 438 of file Types.h.

◆ MorphologySynapseType

enum bioexplorer::morphology::MorphologySynapseType
strong
Enumerator
none 
afferent 
efferent 
debug 
all 

Definition at line 336 of file Types.h.

◆ PopulationColorScheme

enum bioexplorer::morphology::PopulationColorScheme
strong
Enumerator
none 

All nodes use the same color

id 

Colored by id

Definition at line 418 of file Types.h.

Variable Documentation

◆ DEFAULT_ARROW_RADIUS_RATIO

const double bioexplorer::morphology::DEFAULT_ARROW_RADIUS_RATIO = 10.0

Definition at line 63 of file Neurons.cpp.

◆ DEFAULT_DEBUG_SYNAPSE_DENSITY_RATIO

const uint64_t bioexplorer::morphology::DEFAULT_DEBUG_SYNAPSE_DENSITY_RATIO = 5

Definition at line 64 of file Neurons.cpp.

◆ DEFAULT_ENDFOOT_RADIUS_RATIO

const double bioexplorer::morphology::DEFAULT_ENDFOOT_RADIUS_RATIO = 1.1

Definition at line 53 of file Astrocytes.cpp.

◆ DEFAULT_ENDFOOT_RADIUS_SHIFTING_RATIO

const double bioexplorer::morphology::DEFAULT_ENDFOOT_RADIUS_SHIFTING_RATIO = 0.35

Definition at line 54 of file Astrocytes.cpp.

◆ DEFAULT_MITOCHONDRIA_DENSITY

const double bioexplorer::morphology::DEFAULT_MITOCHONDRIA_DENSITY = 0.0459

Definition at line 52 of file Astrocytes.cpp.

◆ DEFAULT_SPINE_RADIUS

const double bioexplorer::morphology::DEFAULT_SPINE_RADIUS = 0.25

Definition at line 32 of file Morphologies.h.

◆ LOADER_NAME

const std::string bioexplorer::morphology::LOADER_NAME = LOADER_ASTROCYTES

Definition at line 42 of file AstrocytesLoader.cpp.

◆ MATERIAL_OFFSET_AFFERENT_SYNAPSE

const size_t bioexplorer::morphology::MATERIAL_OFFSET_AFFERENT_SYNAPSE = 5

Definition at line 40 of file Morphologies.h.

◆ MATERIAL_OFFSET_APICAL_DENDRITE

const size_t bioexplorer::morphology::MATERIAL_OFFSET_APICAL_DENDRITE = 4

Definition at line 39 of file Morphologies.h.

◆ MATERIAL_OFFSET_AXON

const size_t bioexplorer::morphology::MATERIAL_OFFSET_AXON = 2

Definition at line 37 of file Morphologies.h.

◆ MATERIAL_OFFSET_DENDRITE

const size_t bioexplorer::morphology::MATERIAL_OFFSET_DENDRITE = 3

Definition at line 38 of file Morphologies.h.

◆ MATERIAL_OFFSET_EFFERENT_SYNAPSE

const size_t bioexplorer::morphology::MATERIAL_OFFSET_EFFERENT_SYNAPSE = 6

Definition at line 41 of file Morphologies.h.

◆ MATERIAL_OFFSET_END_FOOT

const size_t bioexplorer::morphology::MATERIAL_OFFSET_END_FOOT = 4

Definition at line 45 of file Morphologies.h.

◆ MATERIAL_OFFSET_MICRO_DOMAIN

const size_t bioexplorer::morphology::MATERIAL_OFFSET_MICRO_DOMAIN = 5

Definition at line 46 of file Morphologies.h.

◆ MATERIAL_OFFSET_MITOCHONDRION

const size_t bioexplorer::morphology::MATERIAL_OFFSET_MITOCHONDRION = 7

Definition at line 42 of file Morphologies.h.

◆ MATERIAL_OFFSET_MYELIN_SHEATH

const size_t bioexplorer::morphology::MATERIAL_OFFSET_MYELIN_SHEATH = 9

Definition at line 44 of file Morphologies.h.

◆ MATERIAL_OFFSET_NUCLEUS

const size_t bioexplorer::morphology::MATERIAL_OFFSET_NUCLEUS = 8

Definition at line 43 of file Morphologies.h.

◆ MATERIAL_OFFSET_SOMA

const size_t bioexplorer::morphology::MATERIAL_OFFSET_SOMA = 1

Definition at line 36 of file Morphologies.h.

◆ MATERIAL_OFFSET_VARICOSITY

const size_t bioexplorer::morphology::MATERIAL_OFFSET_VARICOSITY = 0

Definition at line 35 of file Morphologies.h.

◆ MAX_SOMA_RADIUS

const double bioexplorer::morphology::MAX_SOMA_RADIUS = 10.0

Definition at line 65 of file Neurons.cpp.

◆ MITOCHONDRIA_DENSITY

const doubles bioexplorer::morphology::MITOCHONDRIA_DENSITY = {0.0459, 0.0522, 0.064, 0.0774, 0.0575, 0.0403}

Definition at line 76 of file Neurons.cpp.

◆ mitochondrionRadius

const double bioexplorer::morphology::mitochondrionRadius = 0.1

Definition at line 409 of file Types.h.

◆ mitochondrionSegmentSize

const double bioexplorer::morphology::mitochondrionSegmentSize = 0.25

Definition at line 408 of file Types.h.

◆ myelinSteathLength

const double bioexplorer::morphology::myelinSteathLength = 10.0

Definition at line 413 of file Types.h.

◆ myelinSteathRadiusRatio

const double bioexplorer::morphology::myelinSteathRadiusRatio = 3.0

Definition at line 414 of file Types.h.

◆ NB_MATERIALS_PER_MORPHOLOGY

const size_t bioexplorer::morphology::NB_MATERIALS_PER_MORPHOLOGY = 10

Definition at line 34 of file Morphologies.h.

◆ NB_MYELIN_FREE_SEGMENTS

const uint64_t bioexplorer::morphology::NB_MYELIN_FREE_SEGMENTS = 4

Definition at line 62 of file Neurons.cpp.

◆ nbMinSegmentsForVaricosity

const uint64_t bioexplorer::morphology::nbMinSegmentsForVaricosity = 10

Definition at line 416 of file Types.h.

◆ reportTypeAsString

std::map<ReportType, std::string> bioexplorer::morphology::reportTypeAsString
Initial value:
= {{ReportType::undefined, "undefined"},
{ReportType::spike, "spike"},
{ReportType::soma, "soma"},
{ReportType::compartment, "compartment"},
{ReportType::synapse_efficacy, "synapse efficacy"}}

Definition at line 67 of file Neurons.cpp.

◆ SOMA_AS_PARENT

const int64_t bioexplorer::morphology::SOMA_AS_PARENT = -1

Definition at line 48 of file Morphologies.h.

◆ spineRadiusRatio

const double bioexplorer::morphology::spineRadiusRatio = 0.5

Definition at line 411 of file Types.h.

◆ SUPPORTED_PROTOCOL_ASTROCYTES

const std::string bioexplorer::morphology::SUPPORTED_PROTOCOL_ASTROCYTES = "astrocytes://"

Definition at line 43 of file AstrocytesLoader.cpp.

◆ SUPPORTED_PROTOCOL_NEURONS

const std::string bioexplorer::morphology::SUPPORTED_PROTOCOL_NEURONS = "neurons://"

Definition at line 43 of file NeuronsLoader.cpp.