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User Guide

Start with the question you want to answer from spikes, tracking, and behavior. Each route explains the analysis choices and how to interpret the figures.

Choose a Scientific Task

I want to… Start here Check before interpreting
Analyze my recorded spikes and tracking Load NWB data Position units, clocks, unit labels and recording windows
Find where a neuron fires First place field Occupancy, smoothing scale and missing spatial coverage
Compare conditions or trials Place fields on outbound and inbound runs One environment, identical analysis settings, matched unit IDs and observed time in each condition
Classify candidate spatial cells Cell classification Threshold screens versus shuffle evidence
Summarize a population: coverage, remapping, assemblies and reactivation Population analysis Which units passed a spatial screen, bins visited in every condition and one unit selection across periods
Evaluate decoding on new data Held-out decoding Separate training/test periods and locations visited during training
Segment laps and quantify movement Trajectory and behavioral analysis Tracking gaps and invalid positions
Measure speed, heading or position-based features around events Behavior around events Tracking dropouts inside event windows and angle features declared circular
Measure firing around cues Raster and PSTH example Which cues have fully recorded before/after windows
Save results I can interpret later Analysis settings and exports Units, neuron labels, analyzed periods, bin widths and smoothing

Contents

Who This Guide Is For

This guide is for users who:

  • Have completed the Quickstart
  • Want to understand specific features in depth
  • Need to solve complex spatial analysis problems
  • Want to customize neurospatial for their use case

Prerequisites

  • Completed Getting Started section
  • Familiarity with NumPy arrays and basic Python
  • Understanding of spatial coordinates

Each page covers a specific feature area with:

  • Conceptual explanations
  • Code examples
  • Common patterns and best practices
  • Troubleshooting tips

Common Tasks:

See Also