Add automated yearly repo progress report

[CommanderPho]

Analyzed the past 1 year of commits for both this repo and pyPhoPlaceCellAnalysis, extracting and synthesizing scientific motivations, ideas, problems solved, analyses tried, and things ruled out into a markdown table.

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PR created automatically by Jules for task 7715600118527364995 started by @CommanderPho

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[CommanderPho]

Date	Category	Description
2025-06-27	Idea	Conceptualized and implemented novel spatial representations for bidirectional track remapping, allowing for robust cross-epoch comparison of neural activity between distinct long and short track environments.
2025-06-30	Scientific Motivation	Transitioned analytical pipelines to continuous 2D position decoding by default. This change was motivated by the hypothesis that continuous tracking provides a holistic view of place field firing dynamics across multiple interconnected task epochs without artificial segmentation.
2025-07-15	Analysis Tried	Evaluated the efficacy of recursive latent place field decoding during fragmented lap traversals. The goal was to determine if latent neural population structures, decoupled from explicit spatial cues, provide higher-fidelity positional estimates.
2025-07-29	Analysis Tried	Developed comparative scatter analyses contrasting pre-task and post-task neural metrics. Specifically isolated lap duration periods from sharp-wave ripple events to understand state-dependent neural memory consolidation.
2025-07-31	Ruled Out	Abandoned the methodology of reusing active-cell-only computational pipelines for place field tracking. Determined that robust trial-by-trial completion functions require baseline metrics from all recorded neurons to avoid artificially inflated sparsity in decoding.
2025-08-01	Problem Solved	Corrected a critical theoretical flaw in aggregated firing rate distributions where purely directional place cells were erroneously penalized in rate calculations. Implemented distinct left-to-right (LR) and right-to-left (RL) context segmentations to accurately measure directional spatial tuning.
2025-08-07	Idea	Established granular physiological categorizations separating pre- and post-task periods into Theta/Delta and Replay/Delta oscillatory clusters (e.g., ThetaDeltaMinus, ReplayDeltaPlus). This framework was designed to investigate specific neurophysiological correlates with spatial memory consolidation.
2025-08-19	Analysis Tried	Investigated place field stable formation thresholds. Measured the temporal distributions required for initial place field establishment across multiple maze epochs to mathematically define and quantify neural stability criteria.
2025-08-21	Analysis Tried	Quantified trial-by-trial reliability by explicitly charting differences between theoretically measured spatial occupancy and algorithmic decoded occupancy distributions over extended temporal windows.
2025-08-26	Problem Solved	Solidified lap-based pseudo-2D decoding ground-truth validations. Refactored the core computational logic to ensure continuous positional tracking performance is strictly baselined against known, physical animal trajectory intervals.
2025-09-10	Idea	Modularized 2D contextual decoders. Abstracted global epoch temporal boundaries from localized visual tracking bounds, allowing decoders to dynamically handle multiple distinct spatial contexts simultaneously.
2025-09-19	Analysis Tried	Executed comprehensive multi-maze remapping evaluations (comparing consecutive Pre, Maze1, Post1, Maze2, Post2 periods) to empirically assess changes in population firing vectors under controlled, consecutive spatial memory tasks.
2025-09-21	Problem Solved	Fixed critical issues surrounding the parsing and serialization of Population Burst Event (PBE) and ripple decoders, ensuring full reconstruction of historical decoding contexts across independent analysis sessions.