NeuronStudio

NeuronStudio was a non-commercial program created at Icahn School of Medicine at Mount Sinai by the Computational Neurobiology and Imaging Center.

NeuronStudio handled morphologic details on scales spanning local Dendritic spine geometry through complex tree topology to the gross spatial arrangement of multi-neuron networks.

Deconvolution is an image restoration approach where 'a priori' knowledge of the optical system in the form of a point spread function (PSF) is used to obtain a better estimate of the object.

A point spread function can be either calculated from the actual microscope parameters, measured with beads, or estimated and iteratively refined (Blind deconvolution).

In existing skeletonization or vectorization algorithms for dendritic morphometry, the branch cross-section at any node is approximated as circular, with the D6 metric providing the single diameter estimate.

For small structures such as thin dendrites and spines, comprising only a few voxels even at maximal imaging resolution, the error can be significant if this measure is used directly (see figure).

To minimize quantization error and evaluate more precisely the geometry of the nodes, a new estimation technique exists, the Rayburst Sampling Algorithm that uses the original grayscale data rather than the segmented images for precise, continuous radius estimation, and multidirectional radius sampling to more accurately represent non-circular branch cross-sections and non-spherical spine heads.