Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images

By Erik H. W. Meijering, Mathew Jacob, J. Sarria, P. Steiner, H. Hirling, Michael A. Unser. Cytometry Part A, 2004

1,550 citations recorded by the source corpus.

For the investigation of the molecular mechanisms involved in neurite outgrowth and differentiation, accurate and reproducible segmentation and quantification of neuronal processes are a prerequisite. To facilitate this task, we developed a semiautomatic neurite tracing technique. This article describes the design and validation of the technique.

Subfields: Biophysics, Immunology

View Paper: https://www.semanticscholar.org/paper/0fb280a700dffab6f0ee268ca7e2b1480027be9b

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In Biophysics

In Immunology

Erik H. W. Meijering

Citations in the corpus

Stage-Specific Functions of the Small Rho GTPases Cdc42 and Rac1 for Adult Hippocampal Neurogenesis (2013, methodology): “…20 objective (numerical aperture 0.7) on a confocal microscope (Leica SP2 AOBS) at a fixed Z-step of 1.5 m. Z-projections were generated, and total dendritic length was measured in two dimensions using the NeuronJ plugin (Meijering et al., 2004) of NIH ImageJ software (http://imagej.nih.gov/ij/).”
Excitatory GABA Action Is Essential for Morphological Maturation of Cortical Neurons In Vivo (2007, methodology): “D representations, and neurites were traced and quantified with the NeuronJ software (Meijering et al., 2004) (http://rsb.info.nih.gov/ij/).”
Projection onto the Manifold of Elongated Structures for Accurate Extraction (2015, methodology): “They are typically used to compute the Hessian matrix [14, 36, 28, 13, 29] or the Oriented Flux matrix [22, 1, 41, 33, 44], whose eigenvalues then serve to estimate the likelihood that a pixel or voxel lies on a centerline.”
Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes (2011, neutral): “This interface is inspired by that of NeuronJ (Meijering et al., 2004).”
V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets (2010, methodology): “Our method complements existing neuron reconstruction algorithms14,15,16,17,18 in that they can be incorporated as plug-ins so that they could be invoked from V3D, possibly with some guiding marker information, and then their results proofread and corrected in a faster and more accurate way.”
A visual analytics approach to understanding cycling behaviour (2012, neutral): “U d ) which is presented in Figure 11 along with the experimental results of Dai and Faeth [46] ( We =15-150 and ε =680-850).”
Delayed Development of Adult-Generated Granule Cells in Dentate Gyrus (2006, methodology): “Total dendritic length was measured with NeuronJ (Meijering et al., 2004).”
Submitted to Ieee Transactions on Pattern Analysis and Machine Intelligence 1 Multiscale Centerline Detection (neutral): “Most existing techniques rely on filters designed to respond to locally cylindrical structures [15], [24], [27], [35], [44], [58], optimized for specific profiles [22], or learnt [5], [17], [43].”
Neuron tracing in perspective (2010, methodology): “For measuring neurite length parameters in 2D assays, a popular semiautomatic tool is the NeuronJ plugin to ImageJ, whose corresponding article (58) was the highest cited article in the past decade of all those discussed in the present survey (according to the ISI Web of Science).”
Seizures Accelerate Functional Integration of Adult-Generated Granule Cells (2006, neutral): “Total dendritic length and branch point measurements were made with NeuronJ (Meijering et al., 2004).”