Computer Applications in Cell and Neurobiology: A Review

Mize, R. Ranney

doi:10.1016/s0074-7696(08)61488-6

Cited by 11 publications

(1 citation statement)

References 148 publications

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“…In order to apprehend the factors that influence neuronal function beyond inspecting neurons under the microscope, rigorous analysis requires the reconstruction of morphology into measurable representations. Early efforts improved microscope capabilities and integration with computer control and measurement (Glaser and Van Der Loos, 1964; Overdijk et al, 1978), followed by attempts at automated two-dimensional automated neuronal reconstruction (Capowki, 1983; Mize, 1984). In recent history reconstruction has been largely accomplished by manual tracing with camera lucida (Sugihara et al, 1996), through computer interfaces such as Neuromantic (http://www.rdg.ac.uk/neuromantic), Neurolucida (MBF Bioscience; Glaser and Glaser, 1990), and ImageJ plugins (Brown et al, 2005) or even more recently using semi-automated tools like Autoneuron (MBF Bioscience), NeuronStudio (http://research.mssm.edu/cnic), V3D (Peng et al, 2010a), and the TREES toolbox (Cuntz et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

The DIADEM Metric: Comparing Multiple Reconstructions of the Same Neuron

2011

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Digital reconstructions of neuronal morphology are used to study neuron function, development, and responses to various conditions. Although many measures exist to analyze differences between neurons, none is particularly suitable to compare the same arborizing structure over time (morphological change) or reconstructed by different people and/or software (morphological error). The metric introduced for the DIADEM (DIgital reconstruction of Axonal and DEndritic Morphology) Challenge quantifies the similarity between two reconstructions of the same neuron by matching the locations of bifurcations and terminations as well as their topology between the two reconstructed arbors. The DIADEM metric was specifically designed to capture the most critical aspects in automating neuronal reconstructions, and can function in feedback loops during algorithm development. During the Challenge, the metric scored the automated reconstructions of best-performing algorithms against manually traced gold standards over a representative data set collection. The metric was compared with direct quality assessments by neuronal reconstruction experts and with clocked human tracing time saved by automation. The results indicate that relevant morphological features were properly quantified in spite of subjectivity in the underlying image data and varying research goals. The DIADEM metric is freely released open source (http://diademchallenge.org) as a flexible instrument to measure morphological error or change in high-throughput reconstruction projects.

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Section: Introductionmentioning

confidence: 99%

The DIADEM Metric: Comparing Multiple Reconstructions of the Same Neuron

2011

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Morphometric study of the glomerular population in the mouse olfactory bulb: Numerical density and size distribution along the rostrocaudal axis

Royet

Souchier²,

Jourdan

et al. 1988

J of Comparative Neurology

141

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A morphometric study of the glomerular population in the olfactory bulb of the mouse has been carried out by using stereological methods. On the basis of the assumption that the glomerular population is a polydispersed system of spheres, glomerular profile distributions obtained from profile measurements were subjected to a mathematical unfolding procedure to obtain the actual glomerular size distribution. We used a distribution-free method to account for the combined effects of overprojection due to section thickness and truncation (two missing profile mechanisms). Results proved better than those obtained directly from profile measurements without stereological analysis. Several new findings were obtained. First, significant variations of the glomerulus sizes were found along the rostrocaudal axis. The glomeruli are larger in the middle region of the olfactory bulb, whereas their numerical density decreases in the same region. Moreover, the profile density is homogeneous along the rostrocaudal axis. In other words, the relative surface occupied by the periglomerular cells in the glomerular layer is invariant. As a consequence, it may be concluded that the variations in size and numerical density are inversely correlated. Thus, since the glomeruli are larger in the middle region, their number per unit volume is logically smaller in this same area. Finally, the computerization of all these data has led us to estimate the number of glomeruli (1,810 +/- 41) in the olfactory bulb of the mouse. In order to get a comparative idea of their advantages and disadvantages, other standard stereological methods were used in the present study to determine this number. Functional interpretations of the variations of the size and numerical density along the rostrocaudal axis of the olfactory bulb are discussed with respect to ontogenetic and morphofunctional data obtained elsewhere.

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Three-Dimensional Reconstruction Procedure Using GKS Primitives and Software Transformations for Anatomical Studies of the Nervous System

Hornung¹,

Kraftsik²

1988

New Trends in Computer Graphics

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Computer Applications in Cell and Neurobiology: A Review

Cited by 11 publications

References 148 publications

The DIADEM Metric: Comparing Multiple Reconstructions of the Same Neuron

The DIADEM Metric: Comparing Multiple Reconstructions of the Same Neuron

Morphometric study of the glomerular population in the mouse olfactory bulb: Numerical density and size distribution along the rostrocaudal axis

Three-Dimensional Reconstruction Procedure Using GKS Primitives and Software Transformations for Anatomical Studies of the Nervous System

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