Hidden Markov modeling for maximum probability neuron reconstruction

We developed a new technique for automatically tracing out long neuron processes in microscopy images.

T. L. Athey, D. J. Tward, U. Mueller, J. T. Vogelstein, and M. I. Miller, in Communications Biology.
Fitting Splines to Axonal Arbors Quantifies Relationship Between Branch Order and Geometry

We developed a new approach to studying the geometry of axons using data from the MouseLight project.

T. L. Athey, J. Teneggi, J. T. Vogelstein, D. J. Tward, U. Mueller, and M. I. Miller, in Frontiers in Neuroinformatics.
An optimized tissue clearing protocol for rat brain labeling, imaging, and high throughput analysis

Preliminary work analizing large rat brain images using the iDISCO brain clearing protocol.

A. Branch, D. J. Tward, A. C. Kolstad, V. Pulyadi, J. T. Vogelstein, Z. Wu, and M. Gallagher, in bioRxiv.
CloudReg: automatic terabyte-scale cross-modal brain volume registration

Cloud based processing, atlas mapping, and visualization of massive neuroimages for multiple species and modalities.

V. Chandrashekhar, D. J. Tward, D. Crowley, A. K. Crow, M. A. Wright, B. Y. Hsueh, F. Gore, T. A. Machado, A. Branch, J. S. Rosenblum, K. Deisseroth, and J. T. Vogelstein, in Nature methods.
Visualizing synaptic plasticity in vivo by large-scale imaging of endogenous AMPA receptors

We quantified a new fluorescence technique that labels all AMPA receptors int he mouse brain.

A. R. Graves, R. H. Roth, H. L. Tan, Q. Zhu, A. M. Bygrave, E. Lopez-Ortega, I. Hong, A. C. Spiegel, R. C. Johnson, J. T. Vogelstein, D. J. Tward, M. I. Miller, and R. L. Huganir, in Elife.
An optimized protocol for iDISCO+ rat brain clearing, imaging, and analysis
A. Branch, D. Tward, J. T. Vogelstein, Z. Wu, and M. Gallagher, in bioRxiv.