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Figure 4 : Side projection of an in vivo Z -stack of Layer V pyramidal cells in the visual cortex of Thy-1 green fl uorescent protein (GFP) mice taken in SciScan using a Scientifi ca Multiphoton Resonant System.


if it were not moving, while it continues to beat as normal. T e researchers use a synchronization algorithm that analyzes the motion of the heartbeat via simultaneous bright-fi eld illumi- nation. T ey use this synchronization to time the acquisition of a single 2D plane of the heart at a specifi c point in the heartbeat. T e soſt ware then advances the imaging plane to the next step in the Z scan and waits for another trigger when the heart is back in the same position during the next beat. T is will allow the acquisition of 3D two-photon datasets of the beating heart to properly image subcellular structures without motion artifacts. T ese datasets could be used to investigate the details of cell-cell interactions during development or during healing. It could also be used to observe detailed dynamics of the developing valve in the heart.


Active X connectivity . Dr. Jerome Lecoq and Jed Perkins from the Allen Institute for Brain Science use SciScan’s external programmatic control to enable three things: (1) a consistent experience for performing optical physiology on mice across multiple systems. (2) a more natural coordinate system in the context of the targeted visual areas in the mouse. (3) additional functionality not currently available in SciScan. T e data they collect becomes part of the Allen Brain Observatory’s standardized in vivo survey of physiological


2017 September • www.microscopy-today.com


activity in the mouse visual cortex ( http://observatory.brain-map. org/visualcoding ).


Using intrinsic signal imaging, they generate maps of the visual areas for each mouse. T e coordinate system for those maps is developed using a hardware registration scheme that can be shared across all their systems (surgical, intrinsic imaging, and optical physiology). T e users can then target a desired visual area by selecting it with a web tool, which provides the X , Y coordinates of the region in the registration space. T e soſt ware then performs the transformations from those X , Y coordinates into the relative positions of the SciScan coordinate system and issues these new coordinates, through ActiveX, to move the scope into position. T is has another advantage in that safety limits can be set, based on the home position and well size, to prevent moves that would be harmful. Additionally, the exact length of an acquisition is unknown at the time of starting, as it will depend on the stimulus presented and any latency issues in the stimulus system. SciScan doesn’t have built-in support for stopping on a hardware line (it can only start on one). T e researchers from the Allen Institute developed a way of waiting on the trigger line to programmati- cally start SciScan acquiring, and then programmatically cancel the acquisition when the line goes back low.


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