Spine Class Reference

#include <Spine.h>

Collaboration diagram for Spine:

Public Member Functions
double	getAngle (const Eref &e) const
Id	getHead (const Eref &e) const
double	getHeadDiameter (const Eref &e) const
double	getHeadLength (const Eref &e) const
double	getHeadVolume (const Eref &e) const
double	getInclination (const Eref &e) const
double	getMaximumSize (const Eref &e) const
double	getMinimumSize (const Eref &e) const
double	getPsdArea (const Eref &e) const
Id	getShaft (const Eref &e) const
double	getShaftDiameter (const Eref &e) const
double	getShaftLength (const Eref &e) const
double	getTotalLength (const Eref &e) const
void	setAngle (const Eref &e, double theta)
void	setHeadDiameter (const Eref &e, double dia)
void	setHeadLength (const Eref &e, double len)
void	setHeadVolume (const Eref &e, double vol)
void	setInclination (const Eref &e, double phi)
void	setMaximumSize (const Eref &e, double len)
void	setMinimumSize (const Eref &e, double len)
void	setPsdArea (const Eref &e, double area)
void	setShaftDiameter (const Eref &e, double dia)
void	setShaftLength (const Eref &e, double len)
void	setTotalLength (const Eref &e, double len)
	Spine ()
	Spine (const Neuron *parent)

Static Public Member Functions
static const Cinfo *	initCinfo ()

Private Attributes
double	maximumSize_
double	minimumSize_
const Neuron *	parent_

Detailed Description

The Spine is a dendritic spine, typically with 2 compartments, the shaft and the head. It is a FieldElement, so it gets all its values from the parent Neuron. Later we can put in a maturation profile, so that a linear number from 0 to 1 will define all the stages of spine growth from stub to filopodium to mature spine.

Definition at line 24 of file Spine.h.

Constructor & Destructor Documentation

Spine::Spine

(

)

Definition at line 160 of file Spine.cpp.

    : parent_( 0 ),
        minimumSize_( 20.0e-9 ),    // 20 nanometres
        maximumSize_( 10.0e-6 )     // 10 microns
{;}

Spine::Spine

(

const Neuron *

parent

)

Definition at line 166 of file Spine.cpp.

    : parent_( parent ),
        minimumSize_( 20.0e-9 ),    // 20 nanometres
        maximumSize_( 10.0e-6 )     // 10 microns
{;}

Member Function Documentation

double Spine::getAngle

(

const Eref &

e

)

const

Definition at line 381 of file Spine.cpp.

Referenced by initCinfo().

{
    return 0;
}

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Id Spine::getHead

(

const Eref &

e

)

const

double Spine::getHeadDiameter

(

const Eref &

e

)

const

Definition at line 280 of file Spine.cpp.

References Eref::fieldIndex(), parent_, and Neuron::spineIds().

Referenced by getHeadVolume(), getPsdArea(), and initCinfo().

{
    vector< Id > sl = parent_->spineIds( e.fieldIndex() );
    if ( sl.size() > 1 &&
            sl[1].element()->cinfo()->isA( "CompartmentBase" ) )
        return Field< double >::get( sl[1], "diameter" );
    return 0.0;
}

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double Spine::getHeadLength

(

const Eref &

e

)

const

Definition at line 245 of file Spine.cpp.

References Eref::fieldIndex(), parent_, and Neuron::spineIds().

Referenced by getHeadVolume(), getTotalLength(), initCinfo(), and setTotalLength().

{
    vector< Id > sl = parent_->spineIds( e.fieldIndex() );
    if ( sl.size() > 1 &&
                    sl[1].element()->cinfo()->isA( "CompartmentBase" ) )
        return Field< double >::get( sl[1], "length" );
    return 0.0;
}

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double Spine::getHeadVolume

(

const Eref &

e

)

const

Definition at line 325 of file Spine.cpp.

References getHeadDiameter(), getHeadLength(), and PI.

Referenced by initCinfo().

{
    double dia = getHeadDiameter( e );
    return getHeadLength( e ) * dia * dia * PI / 4.0;
}

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double Spine::getInclination

(

const Eref &

e

)

const

Definition at line 391 of file Spine.cpp.

Referenced by initCinfo().

{
    return 0;
}

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double Spine::getMaximumSize

(

const Eref &

e

)

const

Definition at line 411 of file Spine.cpp.

References maximumSize_.

Referenced by initCinfo().

{
    return maximumSize_;
}

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double Spine::getMinimumSize

(

const Eref &

e

)

const

Definition at line 401 of file Spine.cpp.

References minimumSize_.

Referenced by initCinfo().

{
    return minimumSize_;
}

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double Spine::getPsdArea

(

const Eref &

e

)

const

Definition at line 309 of file Spine.cpp.

References getHeadDiameter(), and PI.

Referenced by initCinfo().

{
    double ret = getHeadDiameter( e );
    return ret * ret * PI / 4.0;
}

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Id Spine::getShaft

(

const Eref &

e

)

const

double Spine::getShaftDiameter

(

const Eref &

e

)

const

Definition at line 217 of file Spine.cpp.

References Eref::fieldIndex(), parent_, and Neuron::spineIds().

Referenced by initCinfo().

{
    vector< Id > sl = parent_->spineIds( e.fieldIndex() );
    if ( sl.size() > 0 &&
                sl[0].element()->cinfo()->isA( "CompartmentBase" ) )
        return Field< double >::get( sl[0], "diameter" );
    return 0.0;
}

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double Spine::getShaftLength

(

const Eref &

e

)

const

Definition at line 176 of file Spine.cpp.

References Eref::fieldIndex(), parent_, and Neuron::spineIds().

Referenced by getTotalLength(), initCinfo(), and setTotalLength().

{
    const vector< Id >& sl = parent_->spineIds( e.fieldIndex() );
    if ( sl.size() > 0 &&
                    sl[0].element()->cinfo()->isA( "CompartmentBase" ) )
        return Field< double >::get( sl[0], "length" );
    return 0.0;
}

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double Spine::getTotalLength

(

const Eref &

e

)

const

Definition at line 358 of file Spine.cpp.

References getHeadLength(), and getShaftLength().

Referenced by initCinfo().

{
    return getHeadLength( e ) + getShaftLength( e );
}

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const Cinfo * Spine::initCinfo ( )

static

Definition at line 17 of file Spine.cpp.

References getAngle(), getHeadDiameter(), getHeadLength(), getHeadVolume(), getInclination(), getMaximumSize(), getMinimumSize(), getPsdArea(), getShaftDiameter(), getShaftLength(), getTotalLength(), Neutral::initCinfo(), setAngle(), setHeadDiameter(), setHeadLength(), setHeadVolume(), setInclination(), setMaximumSize(), setMinimumSize(), setPsdArea(), setShaftDiameter(), setShaftLength(), setTotalLength(), and spineCinfo.

Referenced by Neuron::initCinfo().

{
        // Field Definitions
        static ElementValueFinfo< Spine, double > shaftLength (
            "shaftLength",
            "Length of spine shaft.",
            &Spine::setShaftLength,
            &Spine::getShaftLength
        );
        static ElementValueFinfo< Spine, double > shaftDiameter (
            "shaftDiameter",
            "Diameter of spine shaft.",
            &Spine::setShaftDiameter,
            &Spine::getShaftDiameter
        );
        static ElementValueFinfo< Spine, double > headLength (
            "headLength",
            "Length of spine head.",
            &Spine::setHeadLength,
            &Spine::getHeadLength
        );
        static ElementValueFinfo< Spine, double > headDiameter (
            "headDiameter",
            "Diameter of spine head, and also the diameter of the PSD. ",
            &Spine::setHeadDiameter,
            &Spine::getHeadDiameter
        );
        static ElementValueFinfo< Spine, double > psdArea (
            "psdArea",
            "Area of the Post synaptic density, PSD. This is the same as "
            "the cross-section area of spine head, perpendicular to shaft. "
            "Assumes that the head is a cylinder and that its length "
            "does not change. \n"
            "This is useful to scale # of surface molecules on the PSD. ",
            &Spine::setPsdArea,
            &Spine::getPsdArea
        );
        static ElementValueFinfo< Spine, double > headVolume (
            "headVolume",
            "Volume of spine head, treating it as a cylinder. When this is "
            "scaled by the user, both the diameter and the length of the "
            "spine head scale by the cube root of the ratio to the "
            "previous volume. The diameter of the PSD is pegged to the "
            "diameter of the spine head. \n"
            "This is useful to scale total # of molecules in the head. ",
            &Spine::setHeadVolume,
            &Spine::getHeadVolume
        );
        static ElementValueFinfo< Spine, double > totalLength (
            "totalLength",
            "Length of entire spine. Scales both the length of the shaft "
            "and of the spine head, without changing any of the diameters.",
            &Spine::setTotalLength,
            &Spine::getTotalLength
        );
        static ElementValueFinfo< Spine, double > angle (
            "angle",
            "Angle of spine around shaft. Longitude. 0 is away from soma. "
            "Not yet implemented. ",
            &Spine::setAngle,
            &Spine::getAngle
        );
        static ElementValueFinfo< Spine, double > inclination (
            "inclination",
            "inclination of spine with ref to shaft. Normal is 0. "
            "Not yet activated. ",
            &Spine::setInclination,
            &Spine::getInclination
        );
        static ElementValueFinfo< Spine, double > minimumSize (
            "minimumSize",
            "Sanity check for the smallest permitted length or diameter. "
            "Used to avoid unreasonable physiological values, which "
            "are all too easily reached when simulations run unbounded. "
            "Defaults to 20 nanometers, which is somewhat smaller than the "
            "30 nm size estimated for synaptic vesicles. "
            "Does *not* retroactively resize anything. ",
            &Spine::setMinimumSize,
            &Spine::getMinimumSize
        );
        static ElementValueFinfo< Spine, double > maximumSize (
            "maximumSize",
            "Sanity check for the largest permitted length or diameter. "
            "Used to avoid unreasonable physiological values, which "
            "are all too easily reached when simulations run unbounded. "
            "Defaults to 10 microns, which is a pretty monstrous spine. "
            "Does *not* retroactively resize anything. ",
            &Spine::setMaximumSize,
            &Spine::getMaximumSize
        );

        // MsgDest Definitions
        // Shared definitions

        // SrcFinfo Definitions

    static Finfo* spineFinfos[] = {
        &shaftLength,       // Value
        &shaftDiameter,     // Value
        &headLength,        // Value
        &headDiameter,      // Value
        &psdArea,           // Value
        &headVolume,        // Value
        &totalLength,       // Value
    };

    static string doc[] =
    {
            "Name", "Spine",
            "Author", "Upi Bhalla",
            "Description", "Spine wrapper, used to change its morphology "
            "typically by a message from an adaptor. The Spine class "
            "takes care of a lot of resultant scaling to electrical, "
            "chemical, and diffusion properties. "
    };
    static Dinfo< Spine > dinfo;
    static Cinfo spineCinfo (
        "Spine",
        Neutral::initCinfo(),
        spineFinfos,
        sizeof( spineFinfos ) / sizeof ( Finfo* ),
        &dinfo,
        doc,
        sizeof(doc)/sizeof( string ),
        true // This IS a FieldElement, not be be created directly.
    );

    return &spineCinfo;
}

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void Spine::setAngle	(	const Eref &	e,
		double	theta
	)

Definition at line 386 of file Spine.cpp.

Referenced by initCinfo().

{
    ;
}

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void Spine::setHeadDiameter	(	const Eref &	e,
		double	dia
	)

Definition at line 289 of file Spine.cpp.

References Eref::fieldIndex(), Field< A >::get(), maximumSize_, minimumSize_, parent_, Neuron::scaleBufAndRates(), Neuron::scaleHeadDiffusion(), SetGet2< A1, A2 >::set(), and Neuron::spineIds().

Referenced by initCinfo(), and setPsdArea().

{
    if ( dia < minimumSize_ )
        dia = minimumSize_;
    else if ( dia > maximumSize_ )
        dia = maximumSize_;
    vector< Id > sl = parent_->spineIds( e.fieldIndex() );
    if ( sl.size() > 1 &&
            sl[0].element()->cinfo()->isA( "CompartmentBase") )
    {
        double origLen = Field< double >::get( sl[1], "length" );
        double origDia = Field< double >::get( sl[1], "diameter" );
        SetGet2< double, double >::set(
            sl[1], "setGeomAndElec", origLen, dia );
        parent_->scaleHeadDiffusion( e.fieldIndex(), origLen, dia );
        parent_->scaleBufAndRates( e.fieldIndex(),
                        1.0, dia/origDia );
    }
}

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void Spine::setHeadLength	(	const Eref &	e,
		double	len
	)

Definition at line 254 of file Spine.cpp.

References Eref::fieldIndex(), Field< A >::get(), maximumSize_, minimumSize_, parent_, Neuron::scaleBufAndRates(), Neuron::scaleHeadDiffusion(), SetGet2< A1, A2 >::set(), and Neuron::spineIds().

Referenced by initCinfo(), and setTotalLength().

{
    if ( len < minimumSize_ )
        len = minimumSize_;
    else if ( len > maximumSize_ )
        len = maximumSize_;

    vector< Id > sl = parent_->spineIds( e.fieldIndex() );
    if ( sl.size() > 1 &&
                    sl[1].element()->cinfo()->isA( "CompartmentBase") )
    {
        double origDia = Field< double >::get( sl[1], "diameter" );
        double origLen = Field< double >::get( sl[1], "length" );
        SetGet2< double, double >::set(
            sl[1], "setGeomAndElec", len, origDia );
        // Here we've set the electrical and geometrical stuff. Now to
        // do the diffusion.
        // Assume the scaleDiffusion function propagates changes into the
        // VoxelJunctions used by the Dsolve.
        parent_->scaleHeadDiffusion( e.fieldIndex(), len, origDia );
        // Now scale the chem stuff. The PSD mesh is assumed to scale only
        // with top surface area of head, so it is not affected here.
        parent_->scaleBufAndRates( e.fieldIndex(), len/origLen, 1.0 );
    }
}

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void Spine::setHeadVolume	(	const Eref &	e,
		double	vol
	)

Definition at line 332 of file Spine.cpp.

References Eref::fieldIndex(), Field< A >::get(), maximumSize_, minimumSize_, parent_, PI, Neuron::scaleBufAndRates(), Neuron::scaleHeadDiffusion(), SetGet2< A1, A2 >::set(), and Neuron::spineIds().

Referenced by initCinfo().

{
    if ( volume < 0 )
        volume = 0.0;
    double dia = pow( volume * 4.0 / PI, 1.0/3.0 );
    if ( dia < minimumSize_ )
        volume = pow( minimumSize_, 3.0 ) * PI / 4.0;
    else if ( dia > maximumSize_ )
        volume = pow( maximumSize_, 3.0 ) * PI / 4.0;

    vector< Id > sl = parent_->spineIds( e.fieldIndex() );
    if ( sl.size() > 1 &&
            sl[0].element()->cinfo()->isA( "CompartmentBase") )
    {
        double origLen = Field< double >::get( sl[1], "length" );
        double origDia = Field< double >::get( sl[1], "diameter" );
        double oldVolume = origLen * origDia * origDia * PI / 4.0;
        double ratio = pow( volume / oldVolume, 1.0/3.0 );

        SetGet2< double, double >::set(
            sl[1], "setGeomAndElec", origLen * ratio, origDia * ratio );
        parent_->scaleHeadDiffusion( e.fieldIndex(), origLen * ratio, origDia * ratio );
        parent_->scaleBufAndRates( e.fieldIndex(), ratio, ratio );
    }
}

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void Spine::setInclination	(	const Eref &	e,
		double	phi
	)

Definition at line 396 of file Spine.cpp.

Referenced by initCinfo().

{
    ;
}

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void Spine::setMaximumSize	(	const Eref &	e,
		double	len
	)

Definition at line 416 of file Spine.cpp.

References maximumSize_.

Referenced by initCinfo().

{
    maximumSize_ = len;
}

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void Spine::setMinimumSize	(	const Eref &	e,
		double	len
	)

Definition at line 406 of file Spine.cpp.

References minimumSize_.

Referenced by initCinfo().

{
    minimumSize_ = len;
}

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void Spine::setPsdArea	(	const Eref &	e,
		double	area
	)

Definition at line 315 of file Spine.cpp.

References minimumSize_, PI, and setHeadDiameter().

Referenced by initCinfo().

{
    if ( area < 0 ) {
        setHeadDiameter( e, minimumSize_ );
    } else  {
        double dia = 2.0 * sqrt( area / PI );
        setHeadDiameter( e, dia );
    }
}

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void Spine::setShaftDiameter	(	const Eref &	e,
		double	dia
	)

Definition at line 226 of file Spine.cpp.

References Eref::fieldIndex(), Field< A >::get(), maximumSize_, minimumSize_, parent_, Neuron::scaleShaftDiffusion(), SetGet2< A1, A2 >::set(), and Neuron::spineIds().

Referenced by initCinfo().

{
    if ( dia < minimumSize_ )
        dia = minimumSize_;
    else if ( dia > maximumSize_ )
        dia = maximumSize_;

    vector< Id > sl = parent_->spineIds( e.fieldIndex() );
    if ( sl.size() > 1 &&
                    sl[0].element()->cinfo()->isA( "CompartmentBase") )
    {
        double origLen = Field< double >::get( sl[0], "length" );
        SetGet2< double, double >::set(
            sl[0], "setGeomAndElec", origLen, dia );
        // Dia is changing, leave the coords alone.
        parent_->scaleShaftDiffusion( e.fieldIndex(), origLen, dia );
    }
}

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void Spine::setShaftLength	(	const Eref &	e,
		double	len
	)

Definition at line 185 of file Spine.cpp.

References Eref::fieldIndex(), Field< A >::get(), maximumSize_, minimumSize_, parent_, Neuron::scaleShaftDiffusion(), SetGet2< A1, A2 >::set(), SetGet3< A1, A2, A3 >::set(), and Neuron::spineIds().

Referenced by initCinfo(), and setTotalLength().

{
    if ( len < minimumSize_ )
        len = minimumSize_;
    else if ( len > maximumSize_ )
        len = maximumSize_;
    vector< Id > sl = parent_->spineIds( e.fieldIndex() );
    if ( sl.size() > 1 &&
            sl[0].element()->cinfo()->isA( "CompartmentBase" ) )
    {
        double origDia = Field< double >::get( sl[0], "diameter" );
        double dx = Field< double >::get( sl[0], "x" );
        double dy = Field< double >::get( sl[0], "y" );
        double dz = Field< double >::get( sl[0], "z" );
        SetGet2< double, double >::set(
            sl[0], "setGeomAndElec", len, origDia );

        dx = Field< double >::get( sl[0], "x" ) - dx;
        dy = Field< double >::get( sl[0], "y" ) - dy;
        dz = Field< double >::get( sl[0], "z" ) - dz;

        SetGet3< double, double, double >::set( sl[1], "displace",
            dx, dy, dz );
        // Here we've set the electrical and geometrical stuff. Now to
        // do the diffusion. Chem doesn't come into the picture for the
        // spine shaft.
        // Assume the scaleDiffusion function propagates changes into the
        // VoxelJunctions used by the Dsolve.
        parent_->scaleShaftDiffusion( e.fieldIndex(), len, origDia );
    }
}

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void Spine::setTotalLength	(	const Eref &	e,
		double	len
	)

Don't set this if either of them is out of range.

Definition at line 363 of file Spine.cpp.

References getHeadLength(), getShaftLength(), maximumSize_, setHeadLength(), and setShaftLength().

Referenced by initCinfo().

{
    double shaftLen = getShaftLength( e );
    double headLen = getHeadLength( e );
    double totLen = shaftLen + headLen;

    shaftLen *= len / totLen;
    headLen *= len / totLen;

    if ( shaftLen < minimumSize_ || shaftLen > maximumSize_ ||
        headLen < minimumSize_ || headLen > maximumSize_ )
        return;

    setShaftLength( e, shaftLen );
    setHeadLength( e, headLen );
}

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Member Data Documentation

double Spine::maximumSize_

private

Definition at line 86 of file Spine.h.

Referenced by getMaximumSize(), setHeadDiameter(), setHeadLength(), setHeadVolume(), setMaximumSize(), setShaftDiameter(), setShaftLength(), and setTotalLength().

double Spine::minimumSize_

private

Used as a sanity check for assigning dimensions, to avoid unreasonable physiological values. Defaults to 20 nanometers, which is somewhat smaller than the 30 nm size estimated for synaptic vesicles.

Definition at line 85 of file Spine.h.

Referenced by getMinimumSize(), setHeadDiameter(), setHeadLength(), setHeadVolume(), setMinimumSize(), setPsdArea(), setShaftDiameter(), and setShaftLength().

const Neuron* Spine::parent_

private

Definition at line 78 of file Spine.h.

Referenced by getHeadDiameter(), getHeadLength(), getShaftDiameter(), getShaftLength(), setHeadDiameter(), setHeadLength(), setHeadVolume(), setShaftDiameter(), and setShaftLength().

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The documentation for this class was generated from the following files:

• moose-core/biophysics/Spine.h
• moose-core/biophysics/Spine.cpp