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Automatic Robust Neurite Detection and Morphological Analysis of Neuronal Cell Cultures in High-content Screening

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Abstract

Cell-based high content screening (HCS) is becoming an important and increasingly favored approach in therapeutic drug discovery and functional genomics. In HCS, changes in cellular morphology and biomarker distributions provide an information-rich profile of cellular responses to experimental treatments such as small molecules or gene knockdown probes. One obstacle that currently exists with such cell-based assays is the availability of image processing algorithms that are capable of reliably and automatically analyzing large HCS image sets. HCS images of primary neuronal cell cultures are particularly challenging to analyze due to complex cellular morphology. Here we present a robust method for quantifying and statistically analyzing the morphology of neuronal cells in HCS images. The major advantages of our method over existing software lie in its capability to correct non-uniform illumination using the contrast-limited adaptive histogram equalization method; segment neuromeres using Gabor-wavelet texture analysis; and detect faint neurites by a novel phase-based neurite extraction algorithm that is invariant to changes in illumination and contrast and can accurately localize neurites. Our method was successfully applied to analyze a large HCS image set generated in a morphology screen for polyglutamine-mediated neuronal toxicity using primary neuronal cell cultures derived from embryos of a Drosophila Huntington’s Disease (HD) model.

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Acknowledgement

CW and PH are supported by an NIH to PH. JS and JTL are supported by an NIH grant to JTL. We appreciate the kind help of Dr. Xiaobo Zhou and Dr. Shi Peng at the Weill Medical College of Cornell University in using their NeuriteIQ software to generate the neurite tracing results shown in Fig. 11c and d.

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Authors and Affiliations

  1. Department of Computer Science, Brandeis University, Waltham, MA, 02454, USA

    Chaohong Wu & Pengyu Hong

  2. The Picower Institute for Learning and Memory, Departments of Biology and Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA

    Joost Schulte, Katharine J. Sepp & J. Troy Littleton

  3. Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA

    Katharine J. Sepp

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  1. Chaohong Wu
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  5. Pengyu Hong
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Correspondence to Pengyu Hong.

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Wu, C., Schulte, J., Sepp, K.J. et al. Automatic Robust Neurite Detection and Morphological Analysis of Neuronal Cell Cultures in High-content Screening. Neuroinform 8, 83–100 (2010). https://doi.org/10.1007/s12021-010-9067-9

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