SmartScope2: Simultaneous Imaging and Reconstruction of Neuronal Morphology

Abstract

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.

Whole human-brain mapping of single cortical neurons for profiling morphological diversity and stereotypy

“…Now, this dataset is among the largest human singleneuron archives that has been produced. The aggregated production rate of both efficacy in image acquisition over cell injection (54.0% on average, within the range of 25 to 80% depending on the actual human tissue samples) (Materials and Methods) and neuron image production speed (~20 min per neuron) in ex vivo slices was at least 20 times more efficient than our previous cell-injection attempt (e.g., 18).…”

“…Different from several recent successful single-cell morphology studies on model animals such as mouse (11,40) and monkey (41), for human brains, there lacked a suitable large-scale technical platform to conduct similar studies. The pioneering efforts of cell injection, imaging, and morpho-analysis were promising (18,21,24,25,35,(42)(43)(44)(45) yet also had a limited scale for human brains. In comparison with previous approaches, the primary goal of this paper is to provide a generalizable framework for setting up a highthroughput platform of human neuron studies including the modules of cell injection, imaging, neuron tracing, brain registration, pattern analysis, and modeling of neuron morphology and brain anatomy.…”

“…Because the choice of somas for dye injection can be both selective (i.e., applied only to specific neurons or neuron types) and nonspecific (i.e., injection into every possible type of neurons visible in DIC imaging), our approach is capable for targeting and profiling a wide range of neurons adaptively, limited only by the availability of human ex vivo brain slices. Previously, we succeeded in developing ACT for both in vivo single-cell electrophysiology (35) and 3D morphology reconstruction of large human neurons of ex vivo brain slices (18) as well as electroporation-based 3D tracing of in vivo mouse neurons (35). Therefore, a key step to make ACT work for ACTomography is to sample a large enough number of neurons independently to increase the success rate in reconstructing 3D models of neurons, based on limited and often truncated neurites in human brain slices.…”

“…Alternatively, screening of necessarily extracted brain tissues along a surgical path to remove brain tumors and/or other disease sites offers another opportunity to profile states of human brains. Previous efforts such as in vitro single-cell characterization of human brains have started to generate three-dimensional (3D) morphology (18,19), electrophysiology, and transcriptional profiles of single cortical L5 neurons from surgically extracted brain tissues (20). Over the years, large datasets of single-human neuron morphologies consisting of several hundred injected and traced human neurons were documented in frontal, temporal, and occipital cortex (21)(22)(23); anterior temporal lobe (24); and CA1 (25).…”

Real-time targeted illumination in widefield microscopy achieves confocal quality neuronal images

“…Fiber signals in neuron images are typically sparse [22]. In C. elegans neuron imaging, if we divide a 3D z-stack image into submicron voxels, voxels that contain a real fiber occupy less than 1% of total voxels.…”