larvariability-public

Repository with Matlab code and metadata used in Greaney, Heckscher, and Kaufman, J Neurosci (2026; accepted)

Data availability

Raw and preprocessed data can be downloaded from the Figshare project.

To reproduce figures from the paper, download preprocessed data and combine data across larvae using script_combine_fluor_behav.

Certain figures additionally require individual animals' raw video files.

To reproduce panels from a given figure, see corresponding script (e.g., script_Fig1_methods).
Note: Code for some supplementary figures is located in related main figure scripts rather than script_SupplFigs; see script_SupplFigs for locations.

Using the scripts

Before running any script, please first change all file and path locations to match folder locations for your own system.

For post-DeepLabCut data processing and to generate new comboResults structs:

• 1: Run script_clean_relabel
  Allows semi-auto/manual checking of marker placement and converts DLC predicted markers into a struct (cleanedMarkers.mat) for use in the second set of scripts.
  NOTE: If any DLC predictions require fixing, you will need to pause and fix marker positions midway through this script.

• 1.5: Run script_stage_position_extraction, if applicable
  Pulls information about stage movement from a .czi file to use in determining absolute travel distances.

• 2: Run script_behav_results
  Converts cleanedMarkers.mat into a new struct, behavResults.mat, with info about each segment's length over time and the resulting behavioral annotation of locomotor waves.

• 3: Run script_fluor_results, if applicable
  Converts (**) and raw green and red channel tif files into a new struct, fluorResults.mat, with info about each segment's mean & normalized fluorescence over time.

• 4: Run script_combine_fluor_behav
  Consolidates results across multiple larvae into single struct, comboResults.mat, that is used in scripts to generate figures.