Trodes Documentation

This is the official online documentation for Trodes. The user manual will provide a step-by-step guide to getting started with Trodes, setting up a recording session, and more. The development docs will provide details on system architecture, design details, messaging protocols, etc.

Basic

• Quickstart Guide
  • Getting started with SpikeGadgets Main Control Unit (MCU) and Trodes
  • Installing Trodes
  • Creating Your First Workspace in Trodes
  • Setting Up Your Workspace
  • Using Your First Workspace
  • Taking Your First Tethered Recording
  • Viewing Your Data
  • Exporting Your Data
  • Importing Your Data For Further Analysis With Matlab, or Python
• Installing Trodes
  • Connecting to the MCU
  • USB Setup
  • Ethernet Setup
  • Advanced
• Basic Usage
  • Main Interface
  • Source Control
  • The nTrode Panel
  • The Spikes Panel
  • Recording
  • Creating/Opening a Workspace
• Workspaces
  • What is a Workspace?
  • Creating a Workspace Configuration
  • Using the Workspace Editor
  • Auxiliary Display Tab
  • Channel Map Tab
  • Reference Groups Tab
  • Module Configuration Tab
  • Detect/Diagnostics Tab
• Modules
  • Camera Module
  • StateScript
• Exporting Data
  • Export Utility Functions
  • Importing .rec Data Into Matlab or Octave
  • Importing .rec Data Into Python
  • Exporting Camera Module’s Data
• Trodes Export Utility Functions
  • Running from Trodes
  • Altering Export Settings and Channels Using the Workspace
  • Command Line Usage
  • Other Export Utilities
• Neuropixels Headstage
  • Introduction
  • Surgery, Probe Connection & Assembly
  • Probe, Headstage and MCU Configuration
  • Trodes
  • Recording With the Neuropixels Headstage
  • SD Card Setup
  • Synchronization
  • Transferring and Merging Data
• Untethered Recordings Using Datalogging Headstages
  • Overview
  • Synchronization
  • Recording
  • Setting up an Untethered Data Logging Experiment:
  • Transferring Data to Computer and Merging Files
• Untethered Data Synchronization
  • Overview
  • Radio-frequency (RF) Sync Pulses
  • Dropped Packets
  • Drift
• Data Logger GUI
  • Mounting SD Card
  • Updating Control Unit and Headstage Settings
  • Extracting Data and Merging With Environmental Record
  • Process Output
  • SD Card Enable
• SD Card Setup
  • A Note on SD Card Headstage Configuration
  • SD Card Enable
  • SD Card Data Syncing and Merging
• Frequently Asked Questions
  • How do I…

Advanced

• Precision Time Protocol (PTP)
  • Contributors and Sponsors
  • Allied Vision Camera setup
  • Trodes setup
  • Computer and network setup
• Common Average Referencing
  • Opening the group panel
  • Using the CAR groups panel
  • Saving
  • Exporting
• Command Line Options
  • Primary Flags
  • Automatically loading a config or recording
  • Benchmarking
  • Testing
• Network API
  • Real-time Streaming Data From Trodes
  • General Usage
  • Supported Datatypes
  • Preventing frozen execution: non-blocking socket receives or threading
  • Examples
  • Updating your trodesnetwork version via pip
  • Installing trodesnetwork from source
• Benchmarking
  • Enabling Benchmarking
• Workspace XML Format
  • General Info
  • Configuration Flags

Developers

• Developer Documentation
• Setting up the development environment
  • Qt Installation (All platforms)
  • Repository setup
  • Building
  • Platform-specific instructions
• Building
  • Building with CMake on Linux
• Configuration
  • Configuration File
• System Architecture
• Debugging Trodes
  • Compiler errors and warnings
  • Print statements
  • Sanity Check
  • Crash reports
  • Debuggers
  • Valgrind
  • Helgrind
• Networking
  • Timestamping and Synchronization
• TrodesNetwork Python Package
  • Deploying package to PyPi (for maintainers)
• Installing Modules
  • Camera Module
• Camera Module For Developers
  • Networking
• Coding Rules
  • Scope
  • Classes
  • Other C++ Features
  • Coding Style Rules
  • Code Documentations
• Building Documentation
  • Setup
  • Running
  • Contributing

Release notes

• Release Notes
  • 2.3.4
  • 2.3.3
  • 2.3.2
  • 2.3.1
  • 2.3.0
  • 2.2.3
  • 2.2.2
  • 2.2.1
  • 2.2.0
  • 2.1.1
  • 2.1.0
  • 2.0.0
  • 1.9.1
  • 1.9.0
  • 1.8.1
  • 1.8.0
  • 1.7.2 (Mar 27, 2018)
  • 1.6.1 (July 6, 2017)
  • 1.6.0 (June 7, 2017)
  • 1.5.2
  • 1.5.1 (February 28, 2017)
  • 1.5.0 (February 15, 2017)
  • 1.4.2
  • 1.4.1
  • 1.4.0