• NeuriteIQ
  • This release version of NeuriteIQ (Neurite Image Quantitator) software is developed by the Center for Bioengineering and Informatics (CBI, Director: Dr. Stephen Wong), at the Houston Methodist Research Institute. It is a product of interdisciplinary research effort over the years. The bulk of the development effort was done in close collaboration with Junying Yuan's Laboratory at Department of Cell Biology, Harvard Medical School and with Alexei Degterev Laboratory at School of Graduate Biomedical Sciences, Tufts University. We also have a previous version named Neurite, which is developed in collaboration with Professor Liang Ji at Bioinformatics Division, Tsinghua National Laboratory for Information Science and Technology (TNLIST) and Department of Automation, Tsinghua University, China

    The software aims to provide an automated pipeline for quantitative, reproducible, and accurate interpretation of automatic fluorescence microscopy images; in particular, for the labeling and measurement of neurites. NeuriteIQ is a fully automated tool with several parameters being set before the processing. Thus, it is well suitable for batch processing a large dataset of images with little human interference. This research is also funded by NIH R01 LM008696 (S Wong)

    Both single and batch processing functions are provided in NeuriteIQ. In single processing mode, the users can load a specific image and check the result manually after the automated processing. In batch processing mode, the labeling and measurement results are stored in Excel files. Currently, the measurement includes cell number, neuronal cell number, total intensity, average intensity, average area, total neurite length, average neurite length, and neurite brightness, and so on.

    NeuriteIQ is free for use by academia or non-profit organizations and is distributed under the attached license. See NeuriteIQ License.




    The goal of this program is to provide a fully automated method neurite labeling. It is written by Guanglei Xiong at Tsinghua University in collaboration with Drs. Xiaobo Zhou and Stephen Wong at Harvard Medical School.

    As a C++ version of NeuriteIQ, NeuriteLabeler is provided for users who do not use Matlab. NeuriteLabeler is a command line application which can run directly on Windows platform. It gives users an easier way to get a quick view of labeling results of neurite images.

    Note that the program code is implemented in C++ and supports ITK (www.itk.org), VTK (www.vtk.org) and CMake (www.cmake.org). The software package is freely available for academic research. You can run the executable file directly in your Microsoft WINDOWS environment. The source codes are available upon request for academic research.

    Download the software


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