It is now possible to record from hundreds of neurons across multiple brain regions in a single electrophysiology experiment. An essential step in the ensuing data analysis is to assign recorded neurons to the correct brain regions. Brain regions are typically identified after the recordings by comparing images of brain slices to a reference atlas by eye. This introduces error, in particular when slices are not cut at a perfectly coronal angle or when electrode tracks span multiple slices. Here we introduce SHARP-Track, a tool to localize regions of interest and plot the brain regions they pass through. SHARP-Track offers a MATLAB user interface to explore the Allen Mouse Brain Atlas, register asymmetric slice images to the atlas using manual input, and interactively analyze electrode tracks. We find that it reduces error compared to localizing electrodes in a reference atlas by eye. See github.com/cortexlab/allenCCF for the software and wiki.
Highlights d Mice performed an olfactory delayed match to sample (DMS) task by licking left or right d Inactivation of premotor area ALM in the sample and delay periods impaired performance d Signals in upstream areas can be decoded to solve the task, but ALM disregards them d Neurons in layer 2 of ALM represent the identity of the sample odor through the delay
The behavioral strategies that mammals use to learn multi-step routes in natural settings are unknown.Here we show that mice spontaneously adopt a subgoal memory strategy. We first investigated how mice navigate to shelter in response to threats when the direct path is blocked. Initially, they fled toward the shelter and negotiated obstacles using sensory cues. Within twenty minutes, they adopted a subgoal strategy, initiating escapes by running directly to the obstacle's edge. Mice continued to target this subgoal location after the obstacle was removed, indicating use of spatial memory. However, standard models of spatial learningegocentric-movement repetition and internal-map buildingdid not explain how subgoal memories formed.Instead, mice used a hybrid approach: memorizing salient locations encountered during spontaneous 'practice runs'. This strategy was also used during geometrically identical reward-seeking behavior. These results suggest that subgoal memorization is a fundamental strategy by which rodents learn efficient multi-step routes in new environments.learned by observing the structure of the environment, and it depends on the hippocampus 11 . Alternatively, animals can navigate to goals without relying on an internal map. These strategies include integrating self-motion cues to compute a vector back to their starting position 12 ; repeating egocentric movements at familiar junctions 13,14 ; and using landmarks for visual guidance 15 . The latter two tactics, known as "taxon" strategies, are inflexible, rely on proximal cues, and are learned through previous motivated actions 11 . Despite all that is known about rodent navigation, the behavioral strategies that animals spontaneously use to quickly build up and deploy spatial knowledge in new environments remain unknown. The abilities listed above have mostly been demonstrated by repeatedly placing rodents in constrained mazes until they learn to navigate to a goal. In a natural setting, however, spatial learning must occur via internally generated exploration patterns and within a very limited timeframe. It is therefore unclear how well previous classifications of navigation strategies map onto the instincts and learning procedures that animals use during natural goal-directed navigation.Escape behavior offers a powerful model for studying naturalistic navigation in the laboratory. Diverse animals, including fishes, lizards, crabs, birds, and rodents, respond to threats by escaping to a familiar shelter 16 . Mice are known to rapidly identify and memorize shelter locations in new environments and instinctively respond to visual or auditory threats by running straight to the shelter 17,18 . Previous studies have shown that the spatial memory for running back to shelter ('homing') can be based on path integration or distal visual landmarks when a direct path is available 17,[19][20][21] . If the direct path is blocked on one side by a barrier, previous work has shown that gerbils can use spatial memory to reach the hidden shelter after a brief perio...
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