Neural sequences underlying directed turning in Caenorhabditis elegans
Data files
Mar 26, 2026 version files 1.46 GB
-
03072024_N2_2.chxTracks.mat
4.31 MB
-
03072024_N2_3.chxTracks.mat
6.95 MB
-
2023-06-09-01-data.h5
13.82 MB
-
2023-06-09-10-data.h5
13.64 MB
-
2023-06-24-02-data.h5
14.62 MB
-
2023-06-24-11-data.h5
14.56 MB
-
2023-06-24-19-data.h5
13.87 MB
-
2023-06-24-28-data.h5
13.84 MB
-
2023-07-01-01-data.h5
13.37 MB
-
2023-07-01-09-data.h5
12.78 MB
-
2023-07-01-23-data.h5
12.35 MB
-
2023-07-01-30-data.h5
14.46 MB
-
2023-07-07-01-data.h5
11.84 MB
-
2023-07-07-11-data.h5
14.18 MB
-
2023-07-07-18-data.h5
13.67 MB
-
2023-07-08-06-data.h5
14.29 MB
-
2023-07-11-02-data.h5
15.06 MB
-
2023-07-12-01-data.h5
9.67 MB
-
2023-07-13-01-data.h5
14.90 MB
-
2023-07-13-09-data.h5
14 MB
-
2023-07-13-17-data.h5
14.33 MB
-
2023-07-16-02-data.h5
14.44 MB
-
2023-07-28-04-data.h5
14.11 MB
-
2023-08-07-01-data.h5
7.54 MB
-
2023-08-07-08-data.h5
13 MB
-
2023-08-07-16-data.h5
11.45 MB
-
2023-08-18-11-data.h5
15.42 MB
-
2023-08-18-18-data.h5
15.98 MB
-
2023-08-19-01-data.h5
16.19 MB
-
2023-08-22-01-data.h5
9.45 MB
-
2023-08-22-08-data.h5
15.77 MB
-
2023-08-23-02-data.h5
13.16 MB
-
2023-08-23-09-data.h5
15 MB
-
2023-08-23-23-data.h5
15.29 MB
-
2023-08-24-03-data.h5
14.49 MB
-
2023-08-25-02-data.h5
9.31 MB
-
2023-08-25-09-data.h5
14.83 MB
-
2023-08-31-03-data.h5
14.74 MB
-
2023-09-01-01-data.h5
8.26 MB
-
2023-09-02-10-data.h5
15.97 MB
-
2023-09-15-01-data.h5
10.26 MB
-
2023-09-15-08-data.h5
14.24 MB
-
2023-10-03-02-data.h5
8.79 MB
-
2023-10-15-18-data.h5
13.03 MB
-
2024-04-14-06-data.h5
15.05 MB
-
2024-04-15-03-data.h5
13.87 MB
-
2024-04-21-05-data.h5
14.11 MB
-
2024-04-25-07-data.h5
14.51 MB
-
2024-05-02-04-data.h5
15.15 MB
-
2024-05-02-13-data.h5
14.61 MB
-
2024-05-09-13-data.h5
14.26 MB
-
2025-03-10-13-data.h5
11.37 MB
-
2025-03-15-01-data.h5
14.46 MB
-
2025-03-15-09-data.h5
15 MB
-
2025-03-16-01-data.h5
14.44 MB
-
2025-03-17-01-data.h5
15.05 MB
-
2025-03-17-06-data.h5
14.28 MB
-
2025-03-20-01-data.h5
11.15 MB
-
2025-03-20-07-data.h5
10.51 MB
-
2025-04-04-01-data.h5
14.83 MB
-
2025-04-05-01-data.h5
14.54 MB
-
2025-04-05-06-data.h5
15.54 MB
-
2025-04-08-06-data.h5
9.80 MB
-
2025-04-10-02-data.h5
12.31 MB
-
2025-04-14-03-data.h5
14.67 MB
-
2025-04-14-08-data.h5
9.78 MB
-
2025-04-14-14-data.h5
15.39 MB
-
2025-04-15-06-data.h5
14.80 MB
-
2025-04-18-01-data.h5
9.95 MB
-
2025-04-18-06-data.h5
14 MB
-
2025-04-21-07-data.h5
15.74 MB
-
2025-04-21-12-data.h5
14.82 MB
-
2025-04-22-01-data.h5
14.70 MB
-
2025-04-25-01-data.h5
10.11 MB
-
2025-05-01-06-data.h5
9.29 MB
-
diacetyl.wbData.mat
169.75 MB
-
README.md
6.12 KB
-
tdc_enc.csv
7.94 KB
-
tdc1.wbData.mat
59.27 MB
-
tyramine_receptor_expression_normalized.xlsx
27.16 KB
-
wt_enc.csv
7.99 KB
-
wt.wbData.mat
236.93 MB
Abstract
Complex behaviors like navigation rely on sequenced motor outputs that combine to generate effective movement. The brain-wide organization of the circuits that integrate sensory signals to select and execute appropriate motor outputs is not well understood. Here, we characterize the architecture of neural circuits that control C. elegans olfactory navigation. We identify error-correcting turns during navigation and use whole-brain calcium imaging and cell-specific perturbations to determine their neural underpinnings. These turns occur as motor sequences accompanied by neural sequences, in which neurons activate in a stereotyped order during each turn. Distinct cells in this sequence respond to sensory cues, anticipate upcoming turn directions, and drive movement, linking key features of this sensorimotor behavior across time. The neuromodulator tyramine coordinates these sequential brain dynamics. Our results illustrate how neuromodulation can act on a defined neural architecture to generate sequential patterns of activity that link sensory cues to motor actions.
Overview
This contains data and analysis code associated with the study “Neural Sequences Underlying Directed Turning in C. elegans.” This includes behavioral and neural data from whole-brain calcium imaging recordings, behavioral measurements from multi-animal chemotaxis assays, summary encoding datasets used in figure generation, tyramine receptor expression data, and MATLAB scripts used to organize and analyze the data.
Data
Neural data: brain wide imaging data for wild type and tdc-1 datasets can be found as either individual h5 files or MATLAB structures (.mat), both included here. These files have data on both the animal’s behavior (velocity, head curvature) and simultaneous neural activity. MATLAB structures are composed of the information in the .h5 files, with additional information, namely neuron identities for each dataset as well as information about when each animal crosses the octanol or diacetyl gradient. In the MATLAB structures, each row corresponds to one recording/animal, including the name of the .h5 input file corresponding to that animal. In the MATLAB files, wt.wbData.mat contains data from wild type animals encountering octanol, tdc1.wbData.mat contains data from tdc-1 animals encountering octanol, and diacetyl.wbData.mat contains data from wild type animals encountering diacetyl.
Each .h5 file corresponds to one individual whole-brain imaging experiment and contains the neural activity and simultaneous behavioral data for a single animal. The individual h5 files are as follows:
2023-06-09-01-data.h5
2023-06-09-10-data.h5
2023-06-24-02-data.h5
2023-06-24-11-data.h5
2023-06-24-19-data.h5
2023-06-24-28-data.h5
2023-07-01-01-data.h5
2023-07-01-09-data.h5
2023-07-01-23-data.h5
2023-07-01-30-data.h5
2023-07-07-01-data.h5
2023-07-07-11-data.h5
2023-07-07-18-data.h5
2023-07-08-06-data.h5
2023-07-11-02-data.h5
2023-07-12-01-data.h5
2023-07-13-01-data.h5
2023-07-13-09-data.h5
2023-07-13-17-data.h5
2023-07-16-02-data.h5
2023-07-28-04-data.h5
2023-08-07-01-data.h5
2023-08-07-08-data.h5
2023-08-07-16-data.h5
2023-08-18-11-data.h5
2023-08-18-18-data.h5
2023-08-19-01-data.h5
2023-08-22-01-data.h5
2023-08-22-08-data.h5
2023-08-23-02-data.h5
2023-08-23-09-data.h5
2023-08-23-23-data.h5
2023-08-24-03-data.h5
2023-08-25-02-data.h5
2023-08-25-09-data.h5
2023-08-31-03-data.h5
2023-09-01-01-data.h5
2023-09-02-10-data.h5
2023-09-15-01-data.h5
2023-09-15-08-data.h5
2023-10-03-02-data.h5
2023-10-15-18-data.h5
2024-04-14-06-data.h5
2024-04-15-03-data.h5
2024-04-21-05-data.h5
2024-04-25-07-data.h5
2024-05-02-04-data.h5
2024-05-02-13-data.h5
2024-05-09-13-data.h5
2025-03-10-13-data.h5
2025-03-15-01-data.h5
2025-03-15-09-data.h5
2025-03-16-01-data.h5
2025-03-17-01-data.h5
2025-03-17-06-data.h5
2025-03-20-01-data.h5
2025-03-20-07-data.h5
2025-04-04-01-data.h5
2025-04-05-01-data.h5
2025-04-05-06-data.h5
2025-04-08-06-data.h5
2025-04-10-02-data.h5
2025-04-14-03-data.h5
2025-04-14-08-data.h5
2025-04-14-14-data.h5
2025-04-15-06-data.h5
2025-04-18-01-data.h5
2025-04-18-06-data.h5
2025-04-21-07-data.h5
2025-04-21-12-data.h5
2025-04-22-01-data.h5
2025-04-25-01-data.h5
2025-05-01-06-data.h5
Encoding data: wt_enc.csv and tdc_enc.csv report the average encodings for each neuron across all datasets for forwardness, dorsalness, rectifiedness, and EWMA, as defined and described in (Atanas et al. 2023). This data is used in Figure 7A. The file wt_neuron_fraction_encoding.csv gives the fraction of analyzed time segments when each neuron was significantly encoding the above parameters. These values are used in Figure 2 and 4. Expression data can be found in tyramine_receptor_expression_normalized.xlsx, which uses data from (Taylor et al. 2021) to calculate the normalized expression of each tyramine receptor across all neurons. This file is used in Figure S7A.
Code/Software
To analyze behavioral data: save_chemotaxis_data.mat is a MATLAB script that takes in video recordings of animals during chemotaxis and corresponding LinkedTracks files of the centroid position of each worm during that video. The script then outputs a chxData MATLAB structure containing relevant behavioral variables including reorientations, bearing to odor (here called chxAng), and speed.
To analyze neural data: make_WB_struct.mat is a MATLAB script that takes in .h5 files, neuron identifications, and manually scored encounters with the octanol or diacetyl gradient. This script then organizes these inputs into an ouput structure with information about each animal’s behavior and identified neural activity across time.
Details
System requirements: All Matlab scripts were run on Matlab 2022a. Scripts have also been tested on Matlab 2023a.
Installation: Scripts can be run on downloaded data, or data generated from other brain wide imaging datasets using the methods described here and in Atanas 2023. All scripts take <5 minutes to run on a normal desktop computer. The output of the scripts are either a "chxData" or "wbData" file which is a structure containing data from all of the videos processed in this script.
Instructions for use: File names must be provided at the top of the script, do not change any values below the dashed line. File names can be changed depending on the videos that you want to analyze. For “save_chemotaxis_data.mat”, LinkedTrack file names and video recording names must be identical, and LinkedTracks coordinates must be the same as the video coordinates, which is the default of the LinkedTracks output. Here, chxTracks files are provided for ease of use ("03072024_N2_2.chxTracks.mat" and "03072024_N2_3.chxTracks.mat"). These files already have information on the odor coordinates, and these files can then be combined into a chxData structure.
