How to analyse P1

Protocol 1 data is processed automatically after the experiment finishes running in the G4_experiment_conductor. This requires a correctly configured processing_settings.mat file to be present in the protocol folder.

The processing_settings.mat file

This file tells the G4_experiment_conductor how to process the data after the protocol finishes. For Protocol 1, the following fields must be set:

Field Value Description
settings.is_ephys_grid 1 Enables ephys grid processing mode
settings.neutral_frame 1 Frame number of the background/neutral frame
settings.grid_columns [8, 16] Number of columns in the grid for each flash size (6px has 16, 12px has 8)
settings.grid_rows [4, 8] Number of rows in the grid for each flash size (6px has 8, 12px has 4)
settings.path_to_protocol Full path to .g4p file Path including filename and extension
Note

If a variation of P1 uses only one flash size, then grid_columns and grid_rows should be single integers rather than arrays.

What happens automatically

When settings.is_ephys_grid is set to 1, the experiment conductor calls process_data, which in turn runs ephys_grid_processing.m from the G4_Display_Tools repository. This function:

  1. Loads the TDMS log files from the experiment
  2. Extracts the voltage and frame position data
  3. Segments the data by flash position using the frame data
  4. Computes the mean response across repetitions for each flash position
  5. Generates 4 grid plots — one for each combination of flash size and contrast:
    • 12 pixel bright (ON) flashes
    • 12 pixel dark (OFF) flashes
    • 6 pixel bright (ON) flashes
    • 6 pixel dark (OFF) flashes

The processed data is saved as processedData.mat and the plots are saved as GridPlots.fig in the experiment folder.

How to read the grid plots

Each grid plot shows the cell’s voltage response to flashes at every grid position:

  • Subplot position corresponds to the flash location on the arena from the fly’s perspective.
  • Thin lines show responses to individual repetitions.
  • Thick line shows the mean response across all 4 repetitions.
  • Number above each subplot is the frame number of that flash in the pattern file.

Identifying the peak_frame

  1. Look at the 6 pixel flash plots (both bright and dark contrasts).
  2. Identify which subplot has the largest response — this is the flash position closest to the cell’s receptive field centre.
  3. Note the frame number displayed above that subplot. This is your peak_frame.
  4. Also note which contrast (bright or dark) elicited the larger response — this determines whether you run the ON or OFF version of Protocol 2.

When not to proceed to Protocol 2

Consider not running Protocol 2 if:

  • RF near the edge: The peak_frame corresponds to a flash position within ~15 pixels of the arena boundary. The 30 x 30 pixel Protocol 2 area would extend off-screen. The code in generate_protocol2.m will display a warning if this occurs.
  • Weak responses: The voltage deflections are small or inconsistent across repetitions, suggesting the recording quality is poor.
  • No clear RF: No single location shows a clearly stronger response than its neighbours.
  • Recording instability: The baseline voltage drifts significantly across repetitions.