AngleJ: A new tool for the automated measurement of neurite growth orientation in tissue sections

Günther, Manuel Ingo; Günther, Marco; Schneiders, Matthias; Rupp, Rüdiger; Blesch, Armin

doi:10.1016/j.jneumeth.2015.05.021

Cited by 16 publications

(15 citation statements)

References 27 publications

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“…That second through fifth images in Fig. 7 show β III-tubulin labeled axons from the AngleJ paper (Günther et al, 2015), as in Fig. 6, and exhibit comparable values of EMD-alignment score.…”

Section: Resultsmentioning

confidence: 70%

“…This set of data was kindly provided by the lab of Dr. Blesch from the Spinal Cord Injury Center at the Heidelberg University and are part of the images analyzed in the AngleJ paper (Günther et al, 2015). A representative example is shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Current algorithms for the estimation of neurite orientation typically apply smoothing filters to the images, e.g., via Gaussian blurring in the AngleJ method (Günther et al, 2015). This type of data pre-processing, however, while effective at reducing image noise, has a limited impact on other local irregularities.…”

Section: Methodsmentioning

confidence: 99%

“…Its main idea consists in cross-correlating band-passed and rotated versions of the image of interest with a double edge-detection kernel. An alternative approach is the recent AngleJ algorithm by Günther et al (2015), which estimates the orientation of a neurite in an image via convolution against the second order derivative of a Gaussian kernel.…”

Section: Introductionmentioning

confidence: 99%

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Multiscale Analysis of Neurite Orientation and Spatial Organization in Neuronal Images

et al. 2016

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The spatial organization of neurites, the thin processes (i.e., dendrites and axons) that stem from a neuron's soma, conveys structural information required for proper brain function. The alignment, direction and overall geometry of neurites in the brain are subject to continuous remodeling in response to healthy and noxious stimuli. In the developing brain, during neurogenesis or in neuroregeneration, these structural changes are indicators of the ability of neurons to establish axon-to-dendrite connections that can ultimately develop into functional synapses. Enabling a proper quantification of this structural remodeling would facilitate the identification of new phenotypic criteria to classify developmental stages and further our understanding of brain function. However, adequate algorithms to accurately and reliably quantify neurite orientation and alignment are still lacking. To fill this gap, we introduce a novel algorithm that relies on multiscale directional filters designed to measure local neurites orientation over multiple scales. This innovative approach allows us to discriminate the physical orientation of neurites from finer scale phenomena associated with local irregularities and noise. Building on this multiscale framework, we also introduce a notion of alignment score that we apply to quantify the degree of spatial organization of neurites in tissue and cultured neurons. Numerical codes were implemented in Python and released open source and freely available to the scientific community.

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Section: Resultsmentioning

confidence: 70%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Multiscale Analysis of Neurite Orientation and Spatial Organization in Neuronal Images

et al. 2016

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“…The length of GAP-43 positive axons was measured manually in 5 sections from each animal and the result represents the average length for each experimental group. The orientation of GAP-43 positive axons was analyzed by recently developed AngleJ plugin of ImageJ software (Gunther et al 2015a) in 8-bit gray scale images at 20x magnification. Measured angles were pooled into 36 bins between -90° and 90°.…”

Section: Quantification Analysesmentioning

confidence: 99%

Axonal outgrowth stimulation after alginate/mesenchymal stem cell therapy in injured rat spinal cord

Blasko¹,

Szekiova²,

Slovinská³

et al. 2017

Acta Neurobiologiae Experimentalis

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Despite strong efforts in the field, spinal cord trauma still belongs among the untreatable neurological conditions at present.Given the complexity of the nervous system, an effective therapy leading to complete recovery has still not been found. One of the potential tools for supporting tissue regeneration may be found in mesenchymal stem cells, which possess anti-inflammatory and trophic factor-producing properties. In the context of transplantations, application of degradable biomaterials which could form a supportive environment and scaffold to bridge the lesion area represents another attractive strategy. In the present study, through a combination of these two approaches we applied both alginate hydrogel biomaterial alone or allogenic transplants of MSCs isolated from bone marrow seeded in alginate biomaterial into injured rat spinal cord at three weeks after spinal cord compression performed at Th8-9 level. Following three-week survival, using immunohistochemistry we studied axonal growth (GAP-43 expression) and both microglia (Iba-1) and astrocyte (GFAP) reactions at the lesion site and in the segments below and above the lesion. To detect functional improvement, during whole survival period we performed behavioral analyses of locomotor abilities using a classical open field test (BBB score) and a Catwalk automated gait analyzing device (Noldus). We found that despite the absence of locomotor improvement, application of both alginate and MSCs caused significant increase in the number of GAP-43 positive axons.

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Silicon carbide as a highly permissive surface for neural stem cells

Bonaventura

Zimbone

2022

Silicon Carbide Technology for Advanced Human Healthcare Applications

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AngleJ: A new tool for the automated measurement of neurite growth orientation in tissue sections

Cited by 16 publications

References 27 publications

Multiscale Analysis of Neurite Orientation and Spatial Organization in Neuronal Images

Multiscale Analysis of Neurite Orientation and Spatial Organization in Neuronal Images

Axonal outgrowth stimulation after alginate/mesenchymal stem cell therapy in injured rat spinal cord

Silicon carbide as a highly permissive surface for neural stem cells

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