SmartScope2: Simultaneous Imaging and Reconstruction of Neuronal Morphology

Quantitative analysis of neuronal morphology is critical in cell type classification and for deciphering how structure gives rise to function in the brain. Most current approaches to imaging and tracing neuronal 3D morphology are data intensive. We introduce SmartScope2, the first open source, automated neuron reconstruction machine integrating online image analysis with automated multiphoton imaging. SmartScope2 takes advantage of a neuron’s sparse morphology to improve imaging speed and reduce image data stored, transferred and analyzed. We show that SmartScope2 is able to produce the complex 3D morphology of human and mouse cortical neurons with six-fold reduction in image data requirements and three times the imaging speed compared to conventional methods.

[1]  Hanchuan Peng,et al.  Virtual finger boosts three-dimensional imaging and microsurgery as well as terabyte volume image visualization and analysis , 2014, Nature Communications.

[2]  Henry Pinkard,et al.  Micro-Magellan: open-source, sample-adaptive, acquisition software for optical microscopy , 2016, Nature Methods.

[3]  Gene Myers,et al.  Why bioimage informatics matters , 2012, Nature Methods.

[4]  PengHanchuan,et al.  Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model , 2010 .

[5]  Hanchuan Peng,et al.  Extensible visualization and analysis for multidimensional images using Vaa3D , 2014, Nature Protocols.

[6]  Michael S Smirnov,et al.  Automated Remote Focusing, Drift Correction, and Photostimulation to Evaluate Structural Plasticity in Dendritic Spines , 2016, bioRxiv.

[7]  G. Feng,et al.  Acute brain slice methods for adult and aging animals: application of targeted patch clamp analysis and optogenetics. , 2014, Methods in molecular biology.

[8]  Liang Gao,et al.  Imaging multicellular specimens with real-time optimized tiling light-sheet selective plane illumination microscopy , 2016, Nature Communications.

[9]  Eugene W. Myers,et al.  Adaptive light-sheet microscopy for long-term, high-resolution imaging in living organisms , 2016, Nature Biotechnology.

[10]  Peter Saggau,et al.  Compensation of spatial and temporal dispersion for acousto-optic multiphoton laser-scanning microscopy. , 2003, Journal of biomedical optics.

[11]  Hanchuan Peng,et al.  Automatic tracing of ultra-volumes of neuronal images , 2016, Nature Methods.

[12]  Erik Meijering,et al.  Automatic Tracing of Ultra-Volume of Neuronal Images , 2016 .

[13]  Brian R. Long,et al.  Subdiffractive microscopy: techniques, applications, and challenges , 2014, Wiley interdisciplinary reviews. Systems biology and medicine.

[14]  Hanchuan Peng,et al.  TeraFly: real-time three-dimensional visualization and annotation of terabytes of multidimensional volumetric images , 2016, Nature Methods.

[15]  Geoffrey J Evans,et al.  Random-access scanning microscopy for 3D imaging in awake behaving animals , 2016, Nature Methods.

[16]  Hang Zhou,et al.  NeuroGPS-Tree: automatic reconstruction of large-scale neuronal populations with dense neurites , 2015, Nature Methods.

[17]  Hans-Ulrich Dodt,et al.  Light sheet microscopy of living or cleared specimens , 2012, Current Opinion in Neurobiology.

[18]  Qingming Luo,et al.  3D BrainCV: Simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution , 2014, NeuroImage.

[19]  Giorgio A. Ascoli,et al.  Digital Reconstructions of Neuronal Morphology: Three Decades of Research Trends , 2012, Front. Neurosci..

[20]  Hanchuan Peng,et al.  APP2: automatic tracing of 3D neuron morphology based on hierarchical pruning of a gray-weighted image distance-tree , 2013, Bioinform..

[21]  Eugene W. Myers,et al.  Automated Reconstruction of Neuronal Morphology Based on Local Geometrical and Global Structural Models , 2011, Neuroinformatics.

[22]  Pál Maák,et al.  Fast 3D Imaging of Spine, Dendritic, and Neuronal Assemblies in Behaving Animals , 2016, Neuron.

[23]  D. Kleinfeld,et al.  Anatomical and functional imaging of neurons using 2-photon laser scanning microscopy , 1994, Journal of Neuroscience Methods.

[24]  Arjen van Ooyen,et al.  Axonal and dendritic density field estimation from incomplete single-slice neuronal reconstructions , 2014, Front. Neuroanat..