Quickstart

The Nested RF Protocol was designed by LE Burnett in 2024 for patch electrophysiology experiments ran by Jin Yong Park. It was based upon the protocol used in Gruntman et al. 2018. All fly husbandry was carried out by Edward Rogers.

Quick reference

This page provides an overview of the Nested RF Protocol and links to all the guides you need to run and analyse the experiment. If you are setting up for the first time, see the Installation & Setup page, then read Key Concepts for background on the G4 arena coordinate system and terminology.

Protocol overview

Multi-step protocol consisting of a short first protocol (P1) that determines the rough receptive field location and preferred contrast of the cell, and a longer second protocol (P2) that is only presented within a subsection of the arena screen, centred on the location of the peak response determined in P1.
P2 probes the direction selectivity of the cell using moving bar stimuli, as well as measuring the receptive field structure at higher spatial resolution using small flashing squares.
P1 is run through the G4_experiment_conductor GUI
P2 is generated and run through a custom MATLAB script called generate_protocol2().

Aim:

To characterise the receptive field structure and direction selectivity of visual neurons in Drosophila, particularly T4/T5 cells.

The experiments specifically aimed to understand the role of certain proteins linked to specific receptors that are localised to specific locations along the T4/T5 dendrites in shaping the receptive field properties of these cells.

Prerequisites

Before running the protocol, ensure the following are in place:

G4 arena powered on and connected
MATLAB R2023a or later
nested_RF_stimulus repository cloned and src/ folder on the MATLAB path
G4_Display_Tools installed and configured
Circular Statistics Toolbox installed
PanelsController connects to the arena (PanelsController in Command Window)
Protocol 1 .g4p files present in protocols/ folder
Protocol 2 bar patterns present in results/patterns/protocol2/full_field_bars4/

For full installation and configuration details, see the Installation & Setup page.

Protocol descriptions

If you would like to see detailed descriptions of the contents of the two protocols, please see the following pages:

If you would like to see how the parameters of Protocol 1 and 2 have changed over time please see the following page:

Version History

Creating and running the protocols

Experiment log

Find a log of the different experiments and fly strains here:

Experiment Log.

Analysing the data

Experiment workflow

The typical workflow for running the Nested RF Protocol is:

            ┌──────────────────────────┐
            │ Protocol 1 (~6-7.5 min)  │
            │                          │
            │ Run coarse RF mapping    │
            │ using G4_experiment_     │
            │ conductor GUI            │
            └────────────┬─────────────┘
                        │
                        ▼
                    ┌─────────────────────────┐
                    │ Between P1 & P2         │
                    │                         │
                    │ Identify peak_frame     │
                    │ from 6px grid plots.    │
                    │ Determine ON/OFF        │
                    └────────────┬────────────┘
                                │
                                ▼
                            ┌──────────────────────────────┐
                            │ Protocol 2 (~20-25 min)      │
                            │                              │
                            │ Run high-res RF mapping and  │
                            │ direction selectivity via    │
                            │ generate_protocol2()         │
                            └───────────────┬──────────────┘
                                            │
                                            ▼
                                    ┌─────────────────────┐
                                    │ Analysis            │
                                    │                     │
                                    │ process_protocol2() │
                                    │ in experiment folder│
                                    └─────────────────────┘