HippocampalDynamics

This repository contains analysis code for my main PhD project, which is about hippocampal dynamics for associating events across time. It's pretty much work-in-progress. A cleaned-up version of the analysis code will be made available upon publication of the paper.

The olfactory behavioural setup was controlled using my custom-written software SniffinHippo (https://github.com/bumoritz/SniffinHippo).

Project overview

Episodic memory is the ability to remember events in their spatial and temporal context. Forming new episodic memories requires associating events across time and is known to depend on the hippocampus. We investigate whether the hippocampus supports this ability by generating neural activity sequences which tile the temporal gap between events to be linked.

Part 1 - Hippocampal dynamics during learning, retrieval and generalisation

We record the activity of hundreds of neurons in the hippocampus while mice learn and retrieve associations between temporally separated events. To study how the hippocampus generalizes task rules for learning new stimulus associations, we then let expert mice perform the same conceptual task with different stimuli they were never exposed to before.

Part 2 - Binding memories onto artificial memory traces

An emerging view is that binding event representations onto hippocampal sequence templates lays the basis for acquiring new episodic memories. We directly test this hypothesis by stimulating an arbitrary hippocampal sequence while mice have new experiences. We analyze whether this imprinted sequence might acquire meaning to the brain by starting to encode the new experience.

Code structure

For each master script, specify which modules to run in the ops structure and set parameters in the /utils/defaults/get_p.m file.

• Data2repo_Master.m: This master script controls the pre-processing of data from an individual experimental session (e.g. suite2p output, synchronisation data, behaviour data) and saves the relevant information to a repository.
• Repo2repo_Master.m: This master script controls further pre-processing of the data in the repository (e.g. re-identifying photostimulation targets).
• Analyses_Master.m: This master script controls all analyses for individual experimental sessions (e.g. behavioural analysis, sequence analysis, response analysis, follower analysis, imprinting analysis)
• Summary_Master.m: This master script loads in the analysis outputs from all experimental sessions and controls dataset-wide analyses. After importing the relevant analysis outputs using Summary_Master.m, the manuscript figures can be recreated using the scripts in the figures folder.