Automated Sholl analysis of digitized neuronal morphology at multiple scales: Whole cell Sholl analysis versus Sholl analysis of arbor subregions

Abstract

The morphology of dendrites and the axon determines how a neuron processes and transmits information. Neurite morphology is frequently analyzed by Sholl analysis or by counting the total number of neurites and branch tips. However, the time and resources required to perform such analysis by hand is prohibitive for the processing of large data sets and introduces problems with data auditing and reproducibility. Furthermore, analyses performed by hand or using course-grained morphometric data extraction tools can obscure subtle differences in data sets because they do not store the data in a form that facilitates the application of multiple analytical tools. To address these shortcomings, we have developed a program (titled “Bonfire”) to facilitate digitization of neurite morphology and subsequent Sholl analysis. Our program builds upon other available open-source morphological analysis tools by performing Sholl analysis on subregions of the neuritic arbor, enabling the detection of local level changes in dendrite and axon branching behavior. To validate this new tool, we applied Bonfire analysis to images of hippocampal neurons treated with 25 ng/ml Brain-Derived Neurotrophic Factor (BDNF) and untreated control neurons. Consistent with prior findings, conventional Sholl analysis revealed that global exposure to BDNF increases the number of neuritic intersections proximal to the soma. Bonfire analysis additionally uncovers that BDNF treatment affects both root processes and terminal processes with no effect on intermediate neurites. Taken together, our data suggest that global exposure of hippocampal neurons to BDNF results in a reorganization of neuritic segments within their arbors, but not necessarily a change in their number or length. These findings were only made possible by the neurite-specific Sholl data returned by Bonfire analysis.

Distinct effects on the dendritic arbor occur by microbead versus bath administration of brain-derived neurotrophic factor

“…Stimulation of p75 NTR by BDNF is important for developmental axonal pruning [64], supporting the idea that binding of BDNF to this receptor, and potentially TrkB.T1, distally plays an important role in shaping the dendritic arbor by localized but not global BDNF exposure. In contrast, our previous studies suggest that global application of BDNF increases terminal dendrites with no effect on intermediate dendrites [34]. Thus, the mechanism by which the different modes of BDNF stimulation increase dendritic arbor complexity differ.…”

“…We also performed order-specific Sholl analysis (Figure 3; [34,35]), which sheds light on the mechanism behind the observed increases in certain regions of the overall dendritic arbor by categorizing dendrites according to proximity to the cell body, as denoted by order (primary, secondary, or tertiary and above). The labeling scheme used in this study is the one that is most commonly used for Sholl analysis, termed Inside-Out, in which dendrite order increases with distance from the cell body.…”

“…Dendrites were assessed as previously described [33,34,23] using the most common Sholl analysis, also known as the Inside-Out labeling scheme [35]. We used the “Bonfire” program developed by our laboratory to perform semi-automated Sholl analysis with a 6 μm ring interval starting at 9.3 μm from the soma.…”

MicroRNA-181c Ameliorates Cognitive Impairment Induced by Chronic Cerebral Hypoperfusion in Rats

“…The pyramidal cells in the hippocampus CA1 area from Golgi staining slices were selected, and the total length and arborization of dendrites were studied by Sholl analysis as follows [25]: a transparent grid with concentric rings, equivalent to 10 μm apart, was placed over the dendritic picture, and the number of intersections was used to estimate the dendrite arborization. Three to four animals from each group were randomly selected, and five sections from each animal were selected for counting.…”

Multiscale Analysis of Neurite Orientation and Spatial Organization in Neuronal Images

“…This concept is quite novel and conceptually different from other geometric descriptors proposed in the literature for the analysis of vessel-like structures, such as the Sholl (Langhammer et al, 2010; Sholl, 1953) and fractal analysis (Milošević et al, 2005), which were designed to measure the branching density and ramification richness of neurons rather than their alignment properties.…”