Most human activities engage multiple brain regions simultaneously, but our ability to study this is limited by our capability to run experiments. Electrophysiology is the data-collecting technique of placing electrode probes into the brain to record the electrical activity of neurons. Currently, researchers performing electrophysiology use one or two probes. However, to record activity across many regions, researchers must use multiple probes which introduce new kinds of challenges such as ensuring accurate and reproducible positioning of several probes to target specific areas in the brain, managing probe movements to avoid collisions with each other, and preventing probes from breaking during insertion. Brain-wide coverage will require five, ten, or more probes, amplifying the challenges researchers face with just one or two probes at a time. Over the past two years, I have been developing an automation platform that can solve these challenges in electrophysiology. A key innovation is the integration of a computer-vision-based probe tracking system being developed in collaboration with the Allen Institute. This probe tracking system ensures probes can be accurately positioned on brain regions repeatably and detect when probes fail to insert into the brain, so movements are stopped before damage occurs. The automation platform will also route and manage electrode probes during experiments, preventing collisions with each other and the rig. Together these improvements ensure that electrophysiology experiments can be performed in a reliable, safe, and reproducible manner, but perhaps the biggest improvement the platform provides is efficiency. On average, it takes 15 minutes to insert one probe into the brain, meaning brain-wide experiments using eight probes may need two hours to insert manually, increasing stress on subjects unnecessarily. With automation parallelizing the process, we can reduce insertion times from 15 minutes per probe to 15 minutes flat making brain-wide electrophysiology a viable tool in neuroscience.

Dynamics of activity across the cerebral cortex at the mesoscopic scale – coordinated fluctuations of local populations of neurons — are essential to perception and cognition and relevant to computations like sensorimotor integration and goal-directed task engagement. However, understanding direct causal links between population dynamics and behavior requires the ability to manipulate mesoscale activity and observe the effect of manipulation across multiple brain regions simultaneously. Here, we develop a novel system enabling simultaneous recording and manipulation of activity across the dorsal cortex of awake mice, compatible with large-scale electrophysiology from any region across the brain. Transgenic mice expressing the GCaMP calcium sensor are injected systemically with an adeno-associated virus driving expression of the ChrimsonR excitatory opsin. This strategy drives expression of the blue-excited calcium indicator, GCaMP, in excitatory neurons and red-excited Chrimson opsin in inhibitory neurons. The light channels of the imaging and the opsin do not interfere. We demonstrate widefield single-photon calcium imaging and simultaneous galvo-targeted laser stimulation over the entire dorsal cortical surface and find that the spatial and temporal resolution of the stimulus is suitable for targeting many specific cortical regions in short periods of time. The calcium indicator responded to the laser within 30 ms, and the activity returned to baseline within 100 ms after laser offset. The area of effect was as small as 3 mm² for the lowest laser power or as large as 10 mm² for the largest laser power. Moreover, the preparation is stable over many months and is thus well-suited for long-term behavioral experiments. The ability to stimulate and measure anywhere on the dorsal cortical surface of the brain will allow us to design computational models describing how causal manipulation impacts neural dynamics, especially in the context of designing closed-loop systems to control neural activity and behavior. 

Comprehensive brain atlases are an instrumental prerequisite for neuroscientists, akin to geologic and topographic maps for geographers. In providing a spatial reference system, brain atlases allow for navigation to identified brain regions based on anatomical location. However, many standardized mammalian brain atlases have not been quantitatively validated for in vivo accuracy. Observations of various mouse brain atlases in use  reveal numerous inconsistencies and lead to unquantified errors in brain area targeting. My  hypothesis is that existing mouse brain atlases misrepresent real-world coordinates of the in vivo brain within the mouse skull. To test this, I am establishing reliable methods for the systematic measurement of true stereotaxic brain locations and quantification of coordinate discrepancies between the in vivo brain and atlases. Across a cohort of mouse subjects, I optimized the localization of fluorescent dye injections to quantify specific points in the in vivo space. I evaluated fluorescent dye injections using iontophoresis to control dye flow in mouse brain tissue through applied current. This achieved high-contrast fluorescence histochemical detection without diffusion into untargeted brain areas. In addition, I developed an algorithm that maps injection coordinates from histochemical imaging datasets and targeted stereotaxic brain locations to various brain atlas spaces. In our comparison of the average Euclidean distance between mapped real-world injection and targeted location coordinates across three standardized mouse brain atlases, we identified the MRI-based atlas to be the most accurate. Further, I computed and implemented non-negligible 3-dimensional affine transformations to correct discrepancies between the in vivo space and each mouse brain atlas. We expect this work to produce a validated and accurate coordinate system for targeting electrode insertions. This innovation will substantially improve the quality of large-scale data collection in labs around the world.