Experiment 001 — Fungal Electrical Activity Baseline & Analysis Series

October 2025 – November 2025 · EarthTalk Lab

Status: Completed — Analysis Series
Date Range: October 24, 2025 – November 2025
Overview: Comprehensive baseline characterization and stimulus response analysis of fungal electrical activity using ESP32 sensors monitoring a single substrate block.

1. Overview

Experiment 001 represents the foundational series of analyses establishing baseline electrical activity patterns in fungal mycelium and characterizing responses to various stimuli. This experiment series was conducted using ESP32-based sensors (ESPs) monitoring electrode potentials across a single substrate block colonized by fungal mycelium.

The experiment evolved through multiple phases:

1.1 Primary Objectives

  • Baseline Characterization: Establish diurnal electrical activity patterns and identify repeatable "states" in fungal electrical behavior
  • Spatial Analysis: Map electrical activity patterns across different electrode positions to understand spatial coherence
  • Stimulus Response: Characterize how fungal electrical activity responds to controlled stimuli (fungal inoculation, saline injection)
  • Control Validation: Distinguish biological signals from instrumentation artifacts through saline control runs
  • Methodology Development: Establish reproducible processing pipelines for future experiments

1.2 Experimental Setup

  • Substrate: Single fungal substrate block
  • Sensors: ESP32 devices (ESP04, ESP05, ESP08, ESP11, ESP13, ESP14, ESP17) with ADS1115 ADC modules
  • Electrodes: Multiple electrode pairs (a0–a3 channels) monitoring differential potentials
  • Sampling Rate: ~2 seconds per reading
  • Data Storage: InfluxDB time-series database

2. Analysis Series

The Experiment 001 series consists of multiple focused analyses, each addressing specific questions about fungal electrical activity:

Experiment 001 — Diurnal Electrical States (Baseline Analysis)

Date Range: October 24–30, 2025 | Focus: Initial baseline characterization, hourly aggregation, spatial clustering

Established the foundational observation that fungal electrical activity exhibits consistent day–night rhythms and two spatially coherent clusters. Identified data coverage gaps that motivated Experiment 001A. Detailed analysis with hourly cycles, spatial clustering, saline controls, and daily coverage audit.

Experiment 001A — Extended Baseline Window

Date Range: November 6–12, 2025 | Focus: Complete baseline with full data coverage

Repeated baseline analysis on a cleaner dataset with all ESPs online and complete channel coverage. Confirmed spatial clustering patterns and established canonical baseline for future comparisons.

Experiment 001B — ESP Per-Electrode Profiles

Focus: Individual electrode characterization, variance analysis, differential channel analysis

Detailed per-electrode analysis examining individual channel behavior, variance patterns, and differential channel (d01, d23) characteristics. Identified electrode-specific patterns and spatial relationships.

Experiment 001B Extended — Extended Per-Electrode Analysis

Focus: Extended electrode profiling with multiple runs

Extended analysis of per-electrode profiles with multiple experimental runs, providing additional validation and characterization of electrode-specific patterns.

Experiment 001C — Hourly Window Analysis

Focus: Hour-by-hour breakdown, temporal patterns

Granular hourly analysis examining electrical activity patterns across individual hours of the day, providing detailed temporal resolution of diurnal cycles.

Experiment 001D — Stimulus Window Responses

Focus: Fungal inoculation stimulus responses, event-based analysis

Analysis of electrical responses to fungal inoculation events, examining how the system responds to controlled biological stimuli. Event-based windowing around stimulus application times.

Experiment 001E — Daily Swing Baselines

Focus: Daily baseline variations, swing analysis across multiple time windows

Examination of daily baseline variations using multiple time window sizes (5, 10, 30, 60 minutes) to characterize swing patterns and baseline stability across days.

Experiment 001F — Stimulus Amplitude Benchmarks

Focus: Amplitude analysis of stimulus responses, event characterization

Quantitative analysis of stimulus response amplitudes, establishing benchmarks for response magnitude and characterizing amplitude patterns across different events and ESPs.

Experiment 001G — Mock Stimulus Controls

Focus: Control analysis, validation of stimulus protocols

Control analysis using mock stimulus events to validate that observed responses are biological rather than artifacts of the measurement protocol or instrumentation.

3. Timeline & Evolution

3.1 Phase 1: Initial Baseline (October 2025)

  • October 24–30, 2025: Initial baseline data collection (Experiment 001)
  • Discovered data coverage gaps after October 25
  • Identified two spatial clusters in electrical activity
  • Established hourly aggregation methodology

3.2 Phase 2: Extended Baseline (November 2025)

  • November 6–12, 2025: Extended baseline with complete coverage (Experiment 001A)
  • Confirmed spatial clustering patterns
  • Established canonical baseline for future experiments

3.3 Phase 3: Detailed Characterization

  • Experiment 001B: Per-electrode profiling and variance analysis
  • Experiment 001C: Hourly window granular analysis
  • Experiment 001E: Daily swing baseline characterization

3.4 Phase 4: Stimulus Response Analysis

  • Experiment 001D: Fungal inoculation stimulus responses
  • Experiment 001F: Amplitude benchmarking of responses
  • Experiment 001G: Mock stimulus control validation

4. Key Findings

4.1 Diurnal Patterns

  • Fungal electrical activity exhibits consistent day–night rhythms
  • Activity patterns show night-time lull, morning climb, slight noon dip, and evening ramp
  • Patterns are repeatable across multiple days when data coverage is complete

4.2 Spatial Clustering

  • Two distinct spatial clusters identified:
    • Cluster A (Northern Arc): ESP17, ESP14, ESP08
    • Cluster B (Western Block): ESP04, ESP05, ESP11, ESP13
  • Clusters behave almost independently, suggesting semi-independent mycelial regions
  • Clustering patterns consistent across baseline runs

4.3 Stimulus Responses

  • Fungal inoculation events produce measurable electrical responses
  • Response amplitudes vary by ESP location and timing
  • Responses are distinguishable from baseline noise and instrumentation drift

4.4 Control Validation

  • Saline control runs remain largely flat, confirming biological origin of patterns
  • Minor noon dips in saline controls attributed to temperature/evaporation effects
  • Mock stimulus controls validate measurement protocols

5. Methodology

5.1 Data Acquisition

  • Raw voltage readings logged every ~2 seconds per electrode channel
  • Channels monitored: a0, a1, a2, a3 (absolute potentials), d01, d23 (differential)
  • Data exported from InfluxDB to CSV for analysis
  • Timestamps normalized to Costa Rica local time (UTC−6)

5.2 Signal Processing

  • 10-minute window aggregation: Samples partitioned into 10-minute blocks, averaged per electrode
  • Hourly aggregation: 10-minute values grouped by clock hour, averaged across days
  • State mapping: Biological σ calculated by subtracting saline noise in quadrature
  • Event windowing: Time windows extracted around stimulus events for response analysis

5.3 Analysis Tools

  • Python 3.10+ with Pandas, NumPy, Matplotlib
  • Custom scripts for data extraction, aggregation, and visualization
  • InfluxDB for time-series data storage
  • Reproducible processing pipelines documented in analysis scripts

6. Data & Reproducibility

6.1 Data Locations

  • Raw CSVs: analysis/fungal_state_mapping/outputs/experiment_001*/CSV/
  • Derived data: analysis/fungal_state_mapping/outputs/experiment_001*/derived/
  • Plots & assets: experiments/experiment-001*/assets/

6.2 Key Scripts

  • extract_experiment_001_range.py — Data extraction for baseline
  • extract_experiment_001a_range.py — Data extraction for extended baseline
  • generate_experiment_001a_plots.py — Plot generation
  • generate_experiment_001b_plots.py — Per-electrode analysis
  • generate_experiment_001d_windows.py — Stimulus window analysis
  • generate_experiment_001f_amplitude.py — Amplitude analysis
  • And additional scripts for each sub-analysis

6.3 Related Analyses

  • Saline controls: analysis/local_workspace/data_for_professor_Adamatzky/espXX_saline_experiment_*.csv
  • Spatial comparisons: experiments/saline-per-electrode/
  • Spread analysis: experiments/spread-comparison-temp/

7. Future Work & Extensions

7.1 Planned Extensions

  • Hyphal connectivity study to test whether spatial clusters synchronize as connectivity increases
  • Temperature-controlled saline repeat to eliminate thermal drift artifacts
  • Extended stimulus protocols with varied timing and intensity

7.2 Related Experiments

  • Experiment 002: Bean–AMF corridor pilot (plant–fungus interactions)
  • Experiment 003: 10-minute window analysis for specific ESPs

8. References & Documentation

  • EarthTalk Lab internal documentation on electrode calibration and saline baselines (2025)
  • Analysis scripts and processing pipelines in analysis/fungal_state_mapping/scripts/
  • Individual analysis reports linked in Section 2