NeuronMetrics: Software for semi-automated processing of cultured neuron images

Martha L. Narro, Fan Yang, Robert Kraft, Carola Wenk, Alon Efrat, Linda L. Restifo

Research output: Contribution to journalArticlepeer-review

57 Scopus citations


Using primary cell culture to screen for changes in neuronal morphology requires specialized analysis software. We developed NeuronMetrics™ for semi-automated, quantitative analysis of two-dimensional (2D) images of fluorescently labeled cultured neurons. It skeletonizes the neuron image using two complementary image-processing techniques, capturing fine terminal neurites with high fidelity. An algorithm was devised to span wide gaps in the skeleton. NeuronMetrics uses a novel strategy based on geometric features called faces to extract a branch number estimate from complex arbors with numerous neurite-to-neurite contacts, without creating a precise, contact-free representation of the neurite arbor. It estimates total neurite length, branch number, primary neurite number, territory (the area of the convex polygon bounding the skeleton and cell body), and Polarity Index (a measure of neuronal polarity). These parameters provide fundamental information about the size and shape of neurite arbors, which are critical factors for neuronal function. NeuronMetrics streamlines optional manual tasks such as removing noise, isolating the largest primary neurite, and correcting length for self-fasciculating neurites. Numeric data are output in a single text file, readily imported into other applications for further analysis. Written as modules for ImageJ, NeuronMetrics provides practical analysis tools that are easy to use and support batch processing. Depending on the need for manual intervention, processing time for a batch of ∼ 60 2D images is 1.0-2.5 h, from a folder of images to a table of numeric data. NeuronMetrics' output accelerates the quantitative detection of mutations and chemical compounds that alter neurite morphology in vitro, and will contribute to the use of cultured neurons for drug discovery.

Original languageEnglish (US)
Pages (from-to)57-75
Number of pages19
JournalBrain Research
Issue number1
StatePublished - Mar 23 2007


  • Branch count
  • Cell-based assay
  • Convex hull
  • Drosophila
  • Fasciculation
  • Mushroom body
  • Neurite arbor
  • Software development

ASJC Scopus subject areas

  • General Neuroscience
  • Molecular Biology
  • Clinical Neurology
  • Developmental Biology


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