Automated

ORION: Online Reconstruction and functional Imaging Of Neurons: segmentation and tracing of neurons for reconstruction.

A project to develop tools that explore single neuron function via sophisticated image analysis. ORION software bridges advanced optical imaging and compartmental modeling of neuronal function by rapidly, accurately, and robustly generating, from structural image data, a cylindrical morphology model suitable for simulating neuronal function. The goal of this project is to develop a computational and experimental framework to allow real-time mapping of functional imaging data (e.g., spatio-temporal patterns of dendritic voltages or intracellularions) to neuronal structure, during the very limited duration of an acute experiment.

Measures wound-healing assay videos, 

 For each video, the velocity and the order parameter are analyzed in time and space to extract quantitative parameters characterizing the cell motility phenotype. The different conditions (videos) can then be classified according to these parameters.

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.

Computes image Hessian
Based on the algorithm described in the paper below. 

Splines: A Perfect Fit for Signal and Image Processing
M. Unser
IEEE Signal Processing Magazine, vol. 16, no. 6, pp. 22-38, November 1999.
 DOI: 10.1109/79.799930
 http://ieeexplore.ieee.org/document/799930/

Computes image Laplacian

Based on the algorithm described in the paper below. 

Splines: A Perfect Fit for Signal and Image Processing
M. Unser
IEEE Signal Processing Magazine, vol. 16, no. 6, pp. 22-38, November 1999.
 DOI: 10.1109/79.799930
 http://ieeexplore.ieee.org/document/799930/