@article {45064, title = {Virtual finger boosts three-dimensional imaging and microsurgery as well as terabyte volume image visualization and analysis.}, journal = {Nature Communications}, volume = {5}, year = {2014}, month = {2014 Jul 11}, pages = {4342}, abstract = {

Three-dimensional (3D) bioimaging, visualization and data analysis are in strong need of powerful 3D exploration techniques. We develop virtual finger (VF) to generate 3D curves, points and regions-of-interest in the 3D space of a volumetric image with a single finger operation, such as a computer mouse stroke, or click or zoom from the 2D-projection plane of an image as visualized with a computer. VF provides efficient methods for acquisition, visualization and analysis of 3D images for roundworm, fruitfly, dragonfly, mouse, rat and human. Specifically, VF enables instant 3D optical zoom-in imaging, 3D free-form optical microsurgery, and 3D visualization and annotation of terabytes of whole-brain image volumes. VF also leads to orders of magnitude better efficiency of automated 3D reconstruction of neurons and similar biostructures over our previous systems. We use VF to generate from images of 1,107 Drosophila GAL4 lines a projectome of a Drosophila brain.

}, issn = {2041-1723}, doi = {10.1038/ncomms5342}, author = {Peng, Hanchuan and Tang, Jianyong and Xiao, Hang and Bria, Alessandro and Zhou, Jianlong and Butler, Victoria and Zhou, Zhi and Gonzalez-Bellido, Paloma T and Oh, Seung W and Chen, Jichao and Mitra, Ananya and Tsien, Richard W and Zeng, Hongkui and Ascoli, Giorgio A and Iannello, Giulio and Hawrylycz, Michael and Myers, Eugene and Long, Fuhui} } @proceedings {6535, title = {Tracking multiple neurons on worm images.}, volume = {8669}, year = {2013}, month = {2013 Mar}, pages = {86692P}, publisher = {SPIE}, address = {Lake Buena Vista (Orlando Area), Florida, USA}, abstract = {

We are interested in establishing the correspondence between neuron activity and body curvature during various movements of C. Elegans worms. Given long sequences of images, specifically recorded to glow when the neuron is active, it is required to track all identifiable neurons in each frame. The characteristics of the neuron data, e.g., the uninformative nature of neuron appearance and the sequential ordering of neurons, renders standard single and multi-object tracking methods either ineffective or unnecessary for our task. In this paper, we propose a multi-target tracking algorithm that correctly assigns each neuron to one of several candidate locations in the next frame preserving shape constraint. The results demonstrate how the proposed method can robustly track more neurons than several existing methods in long sequences of images.

}, doi = {10.1117/12.2000087}, author = {Paraq, Toufiq and Butler, Victoria and Chklovskii, Dmitri} } @article {5460, title = {Proprioceptive coupling within motor neurons drives C. elegans forward locomotion.}, journal = {Neuron}, volume = {76}, year = {2012}, month = {2012 Nov 21}, pages = {750-61}, abstract = {

Locomotion requires coordinated motor activity throughout an animal{\textquoteright}s body. In both vertebrates and invertebrates, chains of coupled central pattern generators (CPGs) are commonly evoked to explain local rhythmic behaviors. In C.\ elegans, we report that proprioception within the motor circuit is responsible for propagating and coordinating rhythmic undulatory waves from head to tail during forward movement. Proprioceptive coupling between adjacent body regions transduces rhythmic movement initiated near the head into bending waves driven along the body by a chain of reflexes. Using optogenetics and calcium imaging to manipulate and monitor motor circuit activity of moving C.\ elegans held in microfluidic devices, we found that the B-type cholinergic motor neurons transduce the proprioceptive signal. In C.\ elegans, a sensorimotor feedback loop operating within a specific type of motor neuron both drives and organizes body movement.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2012.08.039}, author = {Wen, Quan and Po, Michelle D. and Hulme, Elizabeth and Chen, Sway and Liu, Xinyu and Kwok, Sen Wai and Gershow, Marc and Leifer, Andrew M. and Butler, Victoria and Fang-Yen, Christopher and Kawano, Taizo and Schafer, William R and Whitesides, George and Wyart, Matthieu and Chklovskii, Dmitri B and Samuel, Aravinthan D. T.} }