Innovation

NeuronMetrics: Software for Semi-Automated Processing of Cultured-Neuron Images

University of Arizona
posted on 03/14/2007

Background: Many mutations and drug compounds affect neural function by altering the shape and density of neuron networks, changes that can easily be seen by analyzing still images of prepared neuron cultures that have been genetically altered or exposed to experimental compounds. Drug discovery for developmental brain disorders lags decades behind that in other conditions, however, largely because existing cell-based screening assays are laborious to analyze accurately. A new software application, NeuronMetrics, can greatly improve the speed and accuracy of neuron-culture image analysis, potentially making it possible to process hundreds of such images each day.

Applications:
High-speed analysis of static neuron-culture images for several uses, including
* In vitro screening of potential drug compounds for neural efficacy or toxicity
* In vitro studies of genetic or drug effects on neural-net structure

Advantages:
* Can process roughly 60 two-dimensional images in 60 to 180 minutes
* Complementary to other neuron-image processing software tools * Can analyze certain in vivo images
* Calculated neural “branch counts”from neurite-contact information, improving analysis accuracy
* Automatically “fills”large gaps in the neural network, expanding the accuracy of neural models

The Technology: The invention comprises a software tool, NeuronMetrics, which functions as a set of modules that run in the open-source program ImageJ. NeuronMetrics features a novel method for estimating neural “branch number”(a measure of the axonal complexity) from two-dimensional images. In addition, the tool features a novel method for modeling neural structure in large “gaps”that result from image artifacts. NeuronMetrics and a detailed user guide will be available for download at iBridge. The program is user-friendly and easy to learn, making it a useful screening tool for basic and applied research.

Publication: "Narro, M.L., et al., NeuronMetrics: Software for semi-automated processing of cultured neuron images", Brain Res. (2006)

Advantages

* Processes 60 2D images in 60-150 minutes, depending on complexity. * Estimates neuronal branch counts even if images contain neurite-neurite contacts * Automatically fills gaps in the skeletonized image * Overlays graphic results on original image for quality control * Available at no charge to non-profit organizations * Enhances the value of neuronal cell-based assays for drug * Source code available for customization

Innovation Details
 

Detailed Description

The invention comprises a software tool, NeuronMetrics, which functions as a set of modules that run in the open-source program ImageJ. NeuronMetrics features novel methods for estimating branch number (a measure of neurite arbor complexity) from two-dimensional images, even when they contain neurite-neurite contacts, and for filling large gaps in the skeletonized neuron. NeuronMetrics and a detailed user manual are available for download. NeuronMetrics is user-friendly and easy to learn, making it a useful screening tool for basic and applied research. "PubMed Link":http://www.ncbi.nlm.nih.gov/entrez/q...

Limitations

For Academic Licenses please provide your university-affiliated email address and be prepared to provide a university webpage that demonstrates your affiliation as well.

File Number: UA07-056 

Other Information: * Lead Innovator: Prof. Linda Restifo * Status: in use at the University of Arizona * Refer to: Case # UA07-056 Contact: Lance Creed, JD lcreed@ott.arizona.edu * Publication: Narro et al. (2007). NeuronMetrics: Software for semi-automated processing of cultured neuron images. Brain Research 1138:57-75. PubMed Entry [PMID: 17270152]


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NeuronMetrics(TM) functions as a set of modules that run in the open-source program ImageJ. *Please provide your university-affiliated email add...
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February 11, 2009

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Linda L. Restifo, M.D., Ph.D. - University of Arizona

"I want to say again how happy I am about the iBridge Network mechanism. This seems ideal for NeuronMetrics and I'm very pleased we will be part of this venture."  read more...