Automated and Accurate Detection of Soma Location and Surface Morphology in Large-Scale 3D Neuron Images

Automated and accurate localization and morphometry of somas in 3D neuron images is essential for quantitative studies of neural networks in the brain. However, previous methods are limited in obtaining the location and surface morphology of somas with variable size and uneven staining in large-scale 3D neuron images. In this work, we proposed a method for automated soma locating in large-scale 3D neuron images that contain relatively sparse soma distributions. This method involves three steps: (i) deblocking the image with overlap between adjacent sub-stacks; (ii) locating the somas in each small sub-stack using multi-scale morphological close and adaptive thresholds; and (iii) fusion of the repeatedly located somas in all sub-stacks. We also describe a new method for the accurate detection of the surface morphology of somas containing hollowness; this was achieved by improving the classical Rayburst Sampling with a new gradient-based criteria. Three 3D neuron image stacks of different sizes were used to quantitatively validate our methods. For the soma localization algorithm, the average recall and precision were greater than 93% and 96%, respectively. For the soma surface detection algorithm, the overlap of the volumes created by automatic detection of soma surfaces and manually segmenting soma volumes was more than 84% for 89% of all correctly detected somas. Our method for locating somas can reveal the soma distributions in large-scale neural networks more efficiently. The method for soma surface detection will serve as a valuable tool for systematic studies of neuron types based on neuron structure.     

Variability of adaptational properties of an excitable neuron membrane

This investigation was made on a preparation of stretch receptors of molting crayfish. We made intracellular recordings of potentials from the soma of a slowly-adapting neuron, and extracellular recordings from the nerve trunk. After strychnine had been added to the physiological solution surrounding the preparation, additional rhythmic activity was recorded from the nerve trunk, with corresponding depolarizational oscillations in the membrane potential of the soma of the slowly-adapting neuron. The additional rhythmic activity had a competitive relationship to the action potentials lying along the axon of the slowly-adapting neuron, the rhythm frequency increasing as the prolonged action potentials arose in the soma of that neuron. The depolarizational oscillations in the soma did not change sign as its membrane potential decreased. Analysis of the above phenomenon led to the conclusion that within the axon membrane of a slowly-adapting neuron there appears a section that spontaneously generates rhythmic action potentials. The results of the investigation indicate that there may be wide variations in the adaptational properties of the neuron membrane.Institute of Higher Nervous Activity and Neurophysiology, Academy of Sciences of the USSR, Moscow. Translated from Neirofiziologiya, Vol. 1, No. 3, pp. 309–314, November–December, 1969.     

Excitability of the soma in central nervous system neurons

The ability of the soma of a spinal dorsal horn neuron, a spinal ventral horn neuron (presumably a motoneuron), and a hippocampal pyramidal neuron to generate action potentials was studied using patch-clamp recordings from rat spinal cord slices, the "entire soma isolation" method, and computer simulations. By comparing original recordings from an isolated soma of a dorsal horn neuron with simulated responses, it was shown that computer models can be adequate for the study of somatic excitability. The modeled somata of both spinal neurons were unable to generate action potentials, showing only passive and local responses to current injections. A four- to eightfold increase in the original density of Na(+) channels was necessary to make the modeled somata of both spinal neurons excitable. In contrast to spinal neurons, the modeled soma of the hippocampal pyramidal neuron generated spikes with an overshoot of +9 mV. It is concluded that the somata of spinal neurons cannot generate action potentials and seem to resist their propagation from the axon to dendrites. In contrast, the soma of the hippocampal pyramidal neuron is able to generate spikes. It cannot initiate action potentials in the intact neurons, but it can support their back-propagation from the axon initial segment to dendrites.     

Firing properties of the soma and axon of the abdominal stretch receptor neurons in the crayfish (Astacus leptodactylus)

Action potentials (APs) and impulse responses in the soma and axon of the rapidly and slowly adapting (SA) abdominal stretch receptor neurons of the crayfish (Astacus leptodactylus) were recorded with single microelectrode current-clamp technique. Impulse frequency response to constant current injection was almost constant in the SA neuron while the response decayed completely in the rapidly adapting (RA) neuron. Mean impulse frequency responses to current stimulations were similar in the receptor neuron pairs. In the RA neuron additional current steps evoked additional impulses while a sudden drop in the current amplitude caused adaptation. Impulse duration was dependent on the rate of rise when current ramps were used. Adaptation was facilitated when calculated receptor current was used. Exposing the neuron to 3 mmol/l TEA or scorpion venom resulted in partly elongated impulse responses. SA neuron could continuously convert the current input into impulse frequency irrespective of previous stimulation conditions. Exposing the SA neuron to 3 mmol/l TEA or 1 mmol/l Lidocaine reduced impulse duration to large current stimulations. The SA neuron fired spontaneously if it was exposed to 5-10 mmol/l Lidocaine or 10(-2) mg/ml Leiurus quinquestriatus venom. The action potential (AP) amplitudes in the RA soma, RA axon, SA soma, and SA axon were significantly different between components of all pairs. Duration of the AP in the axon of the RA neuron was significantly shorter than those in the RA soma, SA soma, and SA axon. Diameter of the RA axon was larger than that of the SA axon. Non-adapting impulse responses were promptly observed only in the SA axons. The results indicate that the RA neuron is a sort of rate receptor transducing the rapid length changes in the receptor muscle while the SA neuron is capable of transducing the maintained length changes in the receptor muscle. The differences in firing properties mainly originate from the differences in the active and passive properties of the receptor neurons.     

Neural maintenance roles for the matrix receptor dystroglycan and the nuclear anchorage complex in Caenorhabditis elegans

Recent studies in Caenorhabditis elegans have revealed specific neural maintenance mechanisms that protect soma and neurites against mispositioning due to displacement stresses, such as muscle contraction. We report that C. elegans dystroglycan (DG) DGN-1 functions to maintain the position of lumbar neurons during late embryonic and larval development. In the absence of DGN-1 the cell bodies of multiple lumbar neuron classes are frequently displaced anterior of their normal positions. Early but not later embryonic panneural expression of DGN-1 rescues positional maintenance, suggesting that dystroglycan is required for establishment of a critical maintenance pathway that persists throughout later developmental stages. Lumbar neural maintenance requires only a membrane-tethered N-terminal domain of DGN-1 and may involve a novel extracellular partner for dystroglycan. A genetic screen for similar lumbar maintenance mutants revealed a role for the nesprin/SYNE family protein ANC-1 as well as for the extracellular protein DIG-1, previously implicated in lumbar neuron maintenance. The involvement of ANC-1 reveals a previously unknown role for nucleus-cytoskeleton interactions in neural maintenance. Genetic analysis indicates that lumbar neuron position is maintained in late embryos by parallel DGN-1/DIG-1 and ANC-1-dependent pathways, and in larvae by separate DGN-1 and ANC-1 pathways. The effect of muscle paralysis on late embryonic- or larval-stage maintenance defects in mutants indicates that lumbar neurons are subject to both muscle contraction-dependent and contraction-independent displacement stresses, and that different maintenance pathways may protect against specific types of displacement stress.     

A two-compartment phenomenological model of a dopaminergic neuron

A two-compartment model of a dopaminergic neuron based on modified FitzHugh-Nagumo oscillators for each compartment has been built. The compartments correspond to the soma and dendrites and differ in the values of small parameters. The influence of stimuli (imposed current for the soma compartment and synaptic activation for the dendrite compartment) on the model has been studied. Activation of AMPA and NMDA synaptic currents is shown to cause generation of high-frequency bursts by the neuron. The mechanisms underlying burst generation are considered.     

Virtual NEURON: a strategy for merged biochemical and electrophysiological modeling

Because of its highly branched dendrite, the Purkinje neuron requires significant computational resources if coupled electrical and biochemical activity are to be simulated. To address this challenge, we developed a scheme for reducing the geometric complexity; while preserving the essential features of activity in both the soma and a remote dendritic spine. We merged our previously published biochemical model of calcium dynamics and lipid signaling in the Purkinje neuron, developed in the Virtual Cell modeling and simulation environment, with an electrophysiological model based on a Purkinje neuron model available in NEURON. A novel reduction method was applied to the Purkinje neuron geometry to obtain a model with fewer compartments that is tractable in Virtual Cell. Most of the dendritic tree was subject to reduction, but we retained the neuron’s explicit electrical and geometric features along a specified path from spine to soma. Further, unlike previous simplification methods, the dendrites that branch off along the preserved explicit path are retained as reduced branches. We conserved axial resistivity and adjusted passive properties and active channel conductances for the reduction in surface area, and cytosolic calcium for the reduction in volume. Rallpacks are used to validate the reduction algorithm and show that it can be generalized to other complex neuronal geometries. For the Purkinje cell, we found that current injections at the soma were able to produce similar trains of action potentials and membrane potential propagation in the full and reduced models in NEURON; the reduced model produces identical spiking patterns in NEURON and Virtual Cell. Importantly, our reduced model can simulate communication between the soma and a distal spine; an alpha function applied at the spine to represent synaptic stimulation gave similar results in the full and reduced models for potential changes associated with both the spine and the soma. Finally, we combined phosphoinositol signaling and electrophysiology in the reduced model in Virtual Cell. Thus, a strategy has been developed to combine electrophysiology and biochemistry as a step toward merging neuronal and systems biology modeling.     

Serotonin-immunoreactive neurons in the antennal sensory system of the brain in the carpenter ant, Camponotus japonicus

Social Hymenoptera such as ants or honeybees are known for their extensive behavioral repertories and plasticity. Neurons containing biogenic amines appear to play a major role in controlling behavioral plasticity in these insects. Here we describe the morphology of prominent serotonin-immunoreactive neurons of the antennal sensory system in the brain of an ant, Camponotus japonicus. Immunoreactive fibers were distributed throughout the brain and the subesophageal ganglion (SOG). The complete profile of a calycal input neuron was identified. The soma and dendritic elements are contralaterally located in the lateral protocerebrum. The neuron supplies varicose axon terminals in the lip regions of the calyces of the mushroom body, axon collaterals in the basal ring but not in the collar region, and other axon terminals ipsilaterally in the lateral protocerebrum. A giant neuron innervating the antennal lobe has varicose axon terminals in most of 300 glomeruli in the ventral region of the antennal lobe (AL) and a thick neurite that spans the entire SOG and continues towards the thoracic ganglia. However, neither a soma nor a dendritic element of this neuron was found in the brain or the SOG. A deutocerebral projection neuron has a soma in the lateral cell-body group of the AL, neuronal branches at most of the 12 glomeruli in the dorsocentral region of the ipsilateral AL, and varicose terminal arborizations in both hemispheres of the protocerebrum. Based on the present results, tentative subdivisions in neuropils related to the antennal sensory system of the ant brain are discussed.     

Identification of the cable parameters in the somatic shunt model

 We show that the first five moments of the soma potential and soma current uniquely and stably determine the soma conductance and capacitance and the dendritic electrotonic length, conductance, and capacitance in the so-called somatic shunt model of the passive behavior of a neuron. We test our resulting input admittance algorithm on synthetic data and demonstrate the regularizing effect of knowledge of the ratio of soma to dendrite surface areas. Received: 9 June 1999 / Accepted in revised form: 24 January 2000     

Variations in location and size of identified flight motoneurons in the silk moth,Bombyx mori L. (Lepidoptera : Bombycidae)

Neurons are commonly identified by some specific features. However, recent studies showed variations in identified neurons, which casts doubt on the reliability of neuron identification. This paper tests the anatomical approach that groups of neurons, which look roughly the same in different preparations, really do contain the same neurons; it also tests the reliability of motor neuron identification by cell body size and position of flight motor neurons in the silk moth, Bombyx mori (Lepidoptera : Bombycidae).Soma size and position of 9 motor neurons, which innervate the mesothoracic dorsal longitudinal muscles (DLMs), were quantitatively measured in cobalt back-filled preparations. The neurons were classified into 5 subgroups by soma size and position, and muscle innervation, although neurons in the same subgroup could not be individually identified. The soma size was essentially constant for individual neuron subgroups, but the position varied somewhat. Two subgroups were generally distributed at one position in the ganglion, but others had 2 separate soma areas, and different animals showed different distributions in these 2 areas. These results show that DLM motor neurons can be identified by the soma size and position only when the variation of soma position is examined in advance.     

Identification of Active Membrane Areas in the Giant Neuron of Aplysia

Intracellular and extracellular potentials were simultaneously recorded from the soma and different parts of the axon of the giant cell of Aplysia. Evidence was obtained that for all modes of stimulation the spike originates in the axon at some distance from the cell body. The conduction of the spike is blocked at a distance of 200 to 300 µ from the soma for the antidromic spike, closer to the soma for an orthodromic spike. This event is recorded in the soma as a small or A spike. After some delay, a spike is initiated in the resting part of the axon and in the axon hillock; the soma is invaded only afterwards. The response of these three parts of the neuron is recorded in the soma as the big or S spike.     

The axosomatic contacts on the bursting neuron of the snailHelix pomatia. I. ultrastructural features of the axosomatic contacts

The analysis of serial ultrathin sections of the RPAI bursting neuron of the snail Helix pomatia reveals the presence of axosomatic contacts on its surface membrane. These contacts have a number of specific features: the presynaptic axon contains synaptic vesicles and electron-dense granules, typical of peptidergic terminals; the terminal part of the axon forms many finger-like processes which invaginate the neuronal soma; the width of the cleft (80 nm) in the area of the contact is larger than that in usual synaptic contacts; and there is a system of lacoons in the region of the axosomatic contact; this system is formed by protrusions of the soma and it accompanies the contact along its extent. It is suggested that the system of lacoons which communicates with the space between the terminal and the soma may serve as a ramified synaptic cleft into which the secretion from the terminal is released. This system may contribute to a considerable prolongation of the time of action of the secretory product on the membrane of the RPAI neuron.     

A model for the polarization of neurons by extrinsically applied electric fields.

A model is presented for the subthreshold polarization of a neuron by an applied electric field. It gives insight into how morphological features of a neuron affect its polarizability. The neuronal model consists of one or more extensively branched dendritic trees, a lumped somatic impedance, and a myelinated axon with nodes of Ranvier. The dendritic trees branch according to the 3/2-power rule of Rall, so that each tree has an equivalent cylinder representation. Equations for the membrane potential at the soma and at the nodes of Ranvier, given an arbitrary specified external potential, are derived. The solutions determine the contributions made by the dendritic tree and the axon to the net polarization at the soma. In the case of a spatially constant electric field, both the magnitude and sign of the polarization depend on simple combinations of parameters describing the neuron. One important combination is given by the ratio of internal resistances for longitudinal current spread along the dendritic tree trunk and along the axon. A second is given by the ratio between the DC space constant for the dendritic tree trunk and the distance between nodes of Ranvier in the axon. A third is given by the product of the electric field and the space constant for the trunk of the dendritic tree. When a neuron with a straight axon is subjected to a constant field, the membrane potential decays exponentially with distance from the soma. Thus, the soma seems to be a likely site for action potential initiation when the field is strong enough to elicit suprathreshold polarization. In a simple example, the way in which orientation of the various parts of the neuron affects its polarization is examined. When an axon with a bend is subjected to a spatially constant field, polarization is focused at the bend, and this is another likely site for action potential initiation.     

Transient Response in a Dendritic Neuron Model for Current Injected at One Branch

Mathematical expressions are obtained for the response function corresponding to an instantaneous pulse of current injected to a single dendritic branch in a branched dendritic neuron model. The theoretical model assumes passive membrane properties and the equivalent cylinder constraint on branch diameters. The response function when used in a convolution formula enables one to compute the voltage transient at any specified point in the dendritic tree for an arbitrary current injection at a given input location. A particular numerical example, for a brief current injection at a branch terminal, illustrates the attenuation and delay characteristics of the depolarization peak as it spreads throughout the neuron model. In contrast to the severe attenuation of voltage transients from branch input sites to the soma, the fraction of total input charge actually delivered to the soma and other trees is calculated to be about one-half. This fraction is independent of the input time course. Other numerical examples, which compare a branch terminal input site with a soma input site, demonstrate that, for a given transient current injection, the peak depolarization is not proportional to the input resistance at the injection site and, for a given synaptic conductance transient, the effective synaptic driving potential can be significantly reduced, resulting in less synaptic current flow and charge, for a branch input site. Also, for the synaptic case, the two inputs are compared on the basis of the excitatory post-synaptic potential (EPSP) seen at the soma and the total charge delivered to the soma.     

Helically twisted filaments in giant neurons of a whip spider.

In giant neurons of whip spider legs several filament types are detectable: filaments of 5 to 6 nm thickness as dense masses within the soma of the neuron, an intermediate-sized filament type limited to the dendritic processes forming irregularly wound bundles and finally twisted double filaments in the soma as well as in peripheral regions. The latter are usually aggregated in paracristalloid lattices of different length and diameter.     

Organization of the autophagy pathway in neurons

Macroautophagy (hereafter referred to as autophagy) is an essential quality-control pathway in neurons, which face unique functional and morphological challenges in maintaining the integrity of organelles and the proteome. To overcome these challenges, neurons have developed compartment-specific pathways for autophagy. In this review, we discuss the organization of the autophagy pathway, from autophagosome biogenesis, trafficking, to clearance, in the neuron. We dissect the compartment-specific mechanisms and functions of autophagy in axons, dendrites, and the soma. Furthermore, we highlight examples of how steps along the autophagy pathway are impaired in the context of aging and neurodegenerative disease, which underscore the critical importance of autophagy in maintaining neuronal function and survival.     

Formation of Conditioned Response on Isolated Neurons in the Helix pomatia

The preparation of a completely isolated soma of neurons of molluscs provides the means for more thorough study of the functions of the postsynaptic (somatic) membrane in plastic reorganizations [1,2]. In a previously published work [2], we reported on phenomena of adaptation to the action of a direct electric stimulus in the completely isolated soma of neurons of Helix pomatia. In the present report we shall present the basic results obtained in "associative" learning by an isolated neuron soma.     

Voltage transients in neuronal dendritic trees.

An analytical method is outlined for calculating the passive voltage transient at each point in an extensively branched neuron model for arbitrary current injection at a single branch. The method is based on a convolution formula that employs the transient response function, the voltage response to an instantaneous pulse of current. For branching that satisfies Rall's equivalent cylinder constraint, the response function is determined explicitly. Voltage transients, for a brief current injected at a branch terminal, are evaluated at several locations to illustrate the attenuation and delay characteristics of passive spread. A comparison with the same transient input terminal input, the fraction of input charge dissipated by various branches in the neuron model is illustrated. These fractions are independent of the input time course. For transient synaptic conductance change at a single branch terminal, a numerical example demonstrates the nonlinear effect of reduced synaptic driving potential. The branch terminal synaptic input is compared with the same synaptic conductance input applied to the soma on the basis of excitatory postsynaptic potential amplitude at the soma and charge delivered to the soma.