Automated three-dimensional detection and counting of neuron somata

Oberlaender, Marcel; Dercksen, Vincent J.; Egger, Robert; Gensel, Maria; Sakmann, Bert; Hege, Hans‐Christian

doi:10.1016/j.jneumeth.2009.03.008

Cited by 53 publications

(49 citation statements)

References 40 publications

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“…), a tandem scanning system (Resonance Scanner), Image Processing. NeuN-positive somata were detected in each confocal image stack using a previously described automated counting algorithm (16). Each detected soma is represented by a 3D position landmark.…”

Section: Methodsmentioning

confidence: 99%

“…Each detected soma is represented by a 3D position landmark. The accuracy and robustness of the algorithms has been validated against manual counts performed by expert users (16,24). For detection of GAD67-positive somata, we modified the previously reported automated algorithms to allow for reliable detection independent of the density of GAD67-positive boutons.…”

Section: Methodsmentioning

confidence: 99%

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Cellular organization of cortical barrel columns is whisker-specific

Meyer

Egger

Guest

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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107

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The cellular organization of the cortex is of fundamental importance for elucidating the structural principles that underlie its functions. It has been suggested that reconstructing the structure and synaptic wiring of the elementary functional building block of mammalian cortices, the cortical column, might suffice to reverse engineer and simulate the functions of entire cortices. In the vibrissal area of rodent somatosensory cortex, whisker-related "barrel" columns have been referred to as potential cytoarchitectonic equivalents of functional cortical columns. Here, we investigated the structural stereotypy of cortical barrel columns by measuring the 3D neuronal composition of the entire vibrissal area in rat somatosensory cortex and thalamus. We found that the number of neurons per cortical barrel column and thalamic "barreloid" varied substantially within individual animals, increasing by ∼2.5-fold from dorsal to ventral whiskers. As a result, the ratio between whisker-specific thalamic and cortical neurons was remarkably constant. Thus, we hypothesize that the cellular architecture of sensory cortices reflects the degree of similarity in sensory input and not columnar and/or cortical uniformity principles.T wo major concepts of cortical neuronal organization have been proposed. Structurally, correlations between stereologybased measurements (1) of neuron density and cortical thickness resulted in the hypothesis of structural uniformity, arguing that the number of neurons beneath a square millimeter of cortical surface is constant and independent of cortical area and species (2, 3). Functionally, cortex is organized in a columnar fashion, reflecting similar neuronal activity along the vertical cortex axis in response to peripheral stimuli (4-8). Similar spatial extents of functional cortical columns in the horizontal plane, combined with the idea of cortical uniformity, resulted in the notion that a stereotypic columnar network may also represent the elementary structural building block of sensory cortices (9). In combination, the two concepts thus suggested a common organization of all sensory cortices, which led to reverse engineering and simulation efforts that build up large-scale network models of repeatedly occurring identical cortical circuits (10, 11).The ideal model system for investigating columnar structure and function is the vibrissal area of rodent somatosensory cortex. There, "barrels" of neurons in layer 4 (L4) have been identified as somatotopically organized structural correlates of peripheral receptor organs (i.e., facial whiskers). Whisker/barrel columns have thus been regarded as both structural and functional elementary cortical units (12)(13)(14). To investigate the structural stereotypy of cortical barrel columns, independent of the drawbacks associated with stereology (i.e., extrapolations from small sampling regions), we decided to locate each excitatory and inhibitory neuron soma within the entire volume of interest. Using high-resolution, large-scale confocal microscopy (15) and a...

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Cellular organization of cortical barrel columns is whisker-specific

Meyer

Egger

Guest

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

107

View full text Add to dashboard Cite

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“…To make the exhaustive counting of nerve cells in large tissue volumes feasible, we developed a method for automatic detection and counting of neuron somata in 3D images [15]. It consists of three steps (Fig.…”

Section: Automatic Detection and Counting Algorithmmentioning

confidence: 99%

“…The exact filters and parameters depend on the imaging and staining procedure. In [15] various combinations for different types of image data are presented. Due to locally high cell densities and limited resolution, clusters of touching somata may, however, remain.…”

Section: Automatic Detection and Counting Algorithmmentioning

confidence: 99%

“…Being composed of more than 17.000 neurons [10] of various anatomical as well as functional types, each type displaying complex axonal projection patterns (up to multiple centimeters per neuron), these prerequisites will hardly be satisfied by manual reconstruction approaches. Automated tools that extract the desired anatomical data from microscopic images are hence necessary and were recently described [14,15].…”

Section: Introductionmentioning

confidence: 99%

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Interactive Visualization–A Key Prerequisite for Reconstruction and Analysis of Anatomically Realistic Neural Networks

Dercksen

Oberlaender

Sakmann

et al. 2012

Mathematics and Visualization

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Recent progress in large-volume microscopy, tissue-staining, as well as in image processing methods and 3D anatomy reconstruction allow neuroscientists to extract previously inaccessible anatomical data with high precision. For instance, determination of neuron numbers, 3D distributions and 3D axonal and dendritic branching patterns support recently started efforts to reconstruct anatomically realistic network models of many thousand neurons. Such models aid in understanding neural network structure, and, by numerically simulating electro-physiological signaling, also to reveal their function.We illustrate the impact of visual computing on neurobiology at the example of important steps that are required for the reconstruction of large neural networks. In our case, the network to be reconstructed represents a single cortical column in the rat brain, which processes sensory information from its associated facial whisker hair. We demonstrate how analysis and reconstruction tasks, such as neuron somata counting and tracing of neuronal branches, have been incrementally acceleratedfinally leading to efficiency gains of orders of magnitude. We also show how steps that are difficult to automatize can now be solved interactively with visual support. Additionally, we illustrate how visualization techniques have aided computer scientists during algorithm development. Finally, we present visual analysis techniques allowing neuroscientists to explore morphology and function of 3D neural networks.Altogether, we demonstrate that visual computing techniques make an essential difference in terms of scientific output, both qualitatively, i.e., whether particular goals can be achieved at all, and quantitatively in terms of higher accuracy, faster work-flow and larger scale processing. Such techniques have therefore become essential in the daily work of neuroscientists.

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Morphological characterization of HVC projection neurons in the zebra finch (Taeniopygia guttata)

Benezra

Narayanan

Egger

et al. 2018

J of Comparative Neurology

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Singing behavior in the adult male zebra finch is dependent upon the activity of a cortical region known as HVC (proper name). The vast majority of HVC projection neurons send primary axons to either the downstream premotor nucleus RA (robust nucleus of the arcopallium, or primary motor cortex) or Area X (basal ganglia), which play important roles in song production or song learning, respectively. In addition to these long-range outputs, HVC neurons also send local axon collaterals throughout that nucleus. Despite their implications for a range of circuit models, these local processes have never been completely reconstructed. Here, we use in vivo single-neuron Neurobiotin fills to examine 40 projection neurons across 31 birds with somatic positions distributed across HVC. We show that HVC and HVC neurons have categorically distinct dendritic fields. Additionally, these cell classes send axon collaterals that are either restricted to a small portion of HVC ("local neurons") or broadly distributed throughout the entire nucleus ("broadcast neurons"). Overall, these processes within HVC offer a structural basis for significant local processing underlying behaviorally relevant population activity.

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Automated three-dimensional detection and counting of neuron somata

Cited by 53 publications

References 40 publications

Cellular organization of cortical barrel columns is whisker-specific

Cellular organization of cortical barrel columns is whisker-specific

Interactive Visualization–A Key Prerequisite for Reconstruction and Analysis of Anatomically Realistic Neural Networks

Morphological characterization of HVC projection neurons in the zebra finch (Taeniopygia guttata)

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