AxonTracker =>

  Unraveling the structure and behavior of the brain and central nervous system (CNS) has always been a major goal of neuroscience. Understanding the wiring diagrams of the neuromuscular junction connectomes (full connectivity of nervous system neuronal components) is a starting point for this, as it helps in the study of the organizational and developmental properties of the mammalian CNS. The phenomenon of synapse elimination during developmental stages of the neuronal circuitry is such an example. Due to the organizational specificity of the axons in the connectomes, it becomes important to label and extract individual axons for morphological analysis. Features such as axonal trajectories, their branching patterns, geometric information, the spatial relations of groups of axons, etc. are of great interests for neurobiologists in the study of wiring diagrams. However, due to the complexity of spatial structure of the axons, automatically tracking and reconstructing them from microscopy images in 3D is an unresolved problem. In this article, AxonTracker-3D, an interactive 3D axon tracking and labeling tool is built to obtain quantitative information by reconstruction of the axonal structures in the entire innervation field. The ease of use along with accuracy of results makes AxonTracker-3D an attractive tool to obtain valuable quantitative information from axon datasets.


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AxonTracker 3D software tool was developed by the Center for Bioengineering and Informatics(CBI) at the Methodist Hospital Research Institute in collaboration with Lichtman Group at Department of Molecular and Cellular Biology, Harvard University. The software is useful to semi-automatically track and label axon structures from the motor axon connectome datasets. It is a parameter-free software, and hence can be used over a broad range of datasets.

The software is designed with ease of use in mind. The interface is simple and includes a 3D visualization of the dataset along with a real-time overlay of the tracking results. A 2D view of the dataset is also provided in order to interact with the software. Three orthogonal views are provided with a provision for back-tracking the results. Points can be added/deleted from the tracking results to provide guidance in case of an error.

System Requirements :

Dual Core processor (1.6GHz or faster).

A dedicated graphics card with atleast 128MB of on-chip memory.

Windows XP or later versions.

Download the software

Click here for user Manual

Please refer to this sample video on how to use AxonTracker software.

The download and usage is free for academic and non-commercial purposes and if used in research and publications, it should be referenced..

Center for Bioengineering and Informatics

Center for Bioengineering and Informatics

The mission of the Center for Bioengineering and Informatics (CBI) at Methodist is to engineer better medicine and the tools of biological research and to advance health and biomedical informatics. In doing this, we hope to be a global leader in discovering and creating innovations in drug repositioning and combinations, methods for imaging and probing the body and the brain, devices supporting cellular and molecular diagnostic and therapeutic intervention, and informatics solutions for disease detection, diagnosis, modeling, and prediction. We believe that the fusion of engineering, informatics, and imaging hold the key to translate scientific research effectively and quickly from laboratory bench into patient bedside.

Publications Publications

View select listing of recent publications, journal articles and conference papers.

Software Releases Software Releases

ZFIQ software kit, NeuronIQ, NeuriteIQ, DCellIQ, GCellIQ and AxonTracker software are available now.

About the Director About the Director

Stephen Wong, Ph.D, PE, named director of the bioengineering & informatics program at Methodist.

The research focus of CBI includes:

The development of new methods and tools to identify biomarker motifs and drug leads for combating neurological disorders, cancer, diabetes, and cardiovascular disease.

The development of the next generation devices and instrumentation for on-the-spot diagnosis and molecular image-guided therapy.

Our inter-disciplinary, disease-oriented approach includes the design and integration of multimodal, multiscale imaging techniques, high dimensional biotechnologies, agile medical devices, systems biology, and computational methods to quickly and efficiently acquire, analyze, and digest large volumes of heterogeneous biomedical data and information into knowledge that enables prediction, prevention, detection, diagnosis, and treatment in many areas of human disease. This would represent a profound shift in the practice of medicine and the improved quality of life for patients.

The CBI is part of the Department of Systems Medicine and Bioengineering of The Methodist Hospital Research Institute at The Methodist Hospital in Houston.

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