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An epifluorescence microscope design for naturalistic behavior and cellular activity in freely moving Caenorhabditis elegans.

Code ↔ Paper

2 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 2 matches · 1 of them tie a paragraph to a whole file, not to given lines: a weak match, whose lines are not tinted
  1. [1] § Methods › Calcium imaging in RIA axonal compartments ↔ RIA/7Convert_polar.py, the whole file · a weak match · score 0.72 · polar coordinates, Head angle, atan2, bins, phase, Derivatives
  2. [2] § Methods › Calcium imaging in RIA axonal compartments ↔ RIA/5Midline_Skeletonize.py, lines 158–198 · score 0.57 · Head angle, 0–1, vectors, skeletonized, midline, smoothed

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

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The authors' code

Python · 129 lines · 4.1 KB · no license · 1 match

  1. import pandas as pd
  2. import numpy as np
  3. import matplotlib.pyplot as plt
  4. from pathlib import Path
  6. def convert_to_polar_binned(csv_path, output_path=None):
  7. """
  8. Convert head angle data to polar coordinates and bin into 10-degree sections
  10. Args:
  11. csv_path: Path to input CSV file with head_angle column
  12. output_path: Path to save the output CSV file (optional)
  14. Returns:
  15. DataFrame with the converted data
  16. """
  17. # Load the data
  18. df = pd.read_csv(csv_path)
  20. # Calculate derivative of head_angle (dhead/dt)
  21. head_angle = df['head_angle'].values
  22. dhead_dt = np.gradient(head_angle)
  24. # Calculate polar angle from (head_angle, dhead_dt) using atan2
  25. # atan2(y, x) - head_angle is x, dhead_dt is y
  26. theta = np.arctan2(dhead_dt, head_angle)
  28. # Ensure angles are in [0, 2*pi]
  29. theta = (theta + 2*np.pi) % (2*np.pi)
  31. # Convert to degrees for binning
  32. theta_deg = theta * 180/np.pi
  34. # Create bins from 0 to 360 degrees with 10-degree width
  35. bin_size = 10
  36. bin_edges = np.arange(0, 361, bin_size)
  37. bin_centers = bin_edges[:-1] + bin_size/2
  39. # Find which bin each angle belongs to
  40. bin_indices = np.searchsorted(bin_edges, theta_deg, side='right') - 1
  42. # Handle edge case where theta_deg is exactly 360 degrees
  43. bin_indices[bin_indices == len(bin_edges)-1] = 0
  45. # Get the binned angle (center of the bin)
  46. binned_theta_deg = bin_centers[bin_indices]
  47. binned_theta_rad = binned_theta_deg * np.pi/180
  49. # Calculate x,y coordinates on the unit circle for the binned angles
  50. polar_x = np.cos(binned_theta_rad)
  51. polar_y = np.sin(binned_theta_rad)
  53. # Create a dataframe with the results
  54. result_df = pd.DataFrame({
  55. 'frame': np.arange(len(head_angle)),
  56. 'head_angle': head_angle,
  57. 'dhead_dt': dhead_dt,
  58. 'theta_rad': theta,
  59. 'theta_deg': theta_deg,
  60. 'bin_index': bin_indices,
  61. 'binned_theta_deg': binned_theta_deg,
  62. 'binned_theta_rad': binned_theta_rad,
  63. 'polar_x': polar_x,
  64. 'polar_y': polar_y
  65. })
  67. # Plot the data
  68. plt.figure(figsize=(15, 10))
  70. # Plot the original head angle
  71. plt.subplot(2, 2, 1)
  72. plt.plot(result_df['frame'], result_df['head_angle'])
  73. plt.title('Original Head Angle')
  74. plt.xlabel('Frame')
  75. plt.ylabel('Angle')
  76. plt.grid(True)
  78. # Plot phase space (head_angle vs dhead_dt)
  79. plt.subplot(2, 2, 2)
  80. plt.scatter(result_df['head_angle'], result_df['dhead_dt'],
  81. c=result_df['frame'], cmap='viridis', alpha=0.7)
  82. plt.colorbar(label='Frame')
  83. plt.title('Phase Space: Head Angle vs. dHead/dt')
  84. plt.xlabel('Head Angle')
  85. plt.ylabel('dHead/dt')
  86. plt.grid(True)
  88. # Plot points on the unit circle
  89. plt.subplot(2, 2, 3)
  90. # Draw unit circle
  91. theta_circle = np.linspace(0, 2*np.pi, 100)
  92. plt.plot(np.cos(theta_circle), np.sin(theta_circle), 'k--', alpha=0.3)
  94. # Plot binned points
  95. sc = plt.scatter(result_df['polar_x'], result_df['polar_y'],
  96. c=result_df['frame'], cmap='viridis', alpha=0.7)
  97. plt.colorbar(sc, label='Frame')
  98. plt.title('Binned Polar Coordinates on Unit Circle')
  99. plt.xlabel('X')
  100. plt.ylabel('Y')
  101. plt.axis('equal')
  102. plt.grid(True)
  104. # Plot binned angles over time
  105. plt.subplot(2, 2, 4)
  106. plt.scatter(result_df['frame'], result_df['binned_theta_deg'],
  107. c=result_df['frame'], cmap='viridis', alpha=0.7)
  108. plt.title('Binned Polar Angles')
  109. plt.xlabel('Frame')
  110. plt.ylabel('Angle (degrees)')
  111. plt.grid(True)
  112. plt.ylim(0, 360)
  114. plt.tight_layout()
  115. plt.show()
  117. # Save to a new CSV file
  118. if output_path:
  119. result_df.to_csv(output_path, index=False)
  120. print(f"Data saved to {output_path}")
  122. return result_df
  124. if __name__ == "__main__":
  125. # Replace with actual path to your input CSV file
  126. input_path = "angles/1_angle_smooth.csv" # Update this with your file path
  127. output_path = "angles/1_polar.csv"
  129. result_df = convert_to_polar_binned(input_path, output_path)

7Convert_polar.py at commit 39a954a, no license · at the source

Overview

Authors: Sebastian N. Wittekindt1, Hannah Owens1, Aurélie Guisnet2, Lennard Wittekindt3, Michael Hendricks2
ORCID iDs: Aurélie Guisnet, Michael Hendricks
  1. Integrated Program in Neuroscience, McGill University,Montreal, QC Canada
  2. Department of Biology, McGill University,Montreal, QC Canada
  3. Independent Researcher, Immenreich, Lindau, Germany
Institutions: McGill University (Canada)
Journal: Nature communications, volume 17, issue 1, article 4411
Dates: received 2 May 2025; accepted 23 April 2026; published online 19 May 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1038/s41467-026-72709-w · PMID 42156741 · PMCID PMC13187321 · OpenAlex W7161623035
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: histology / microscopy (modality), C. elegans (organism), cellular / molecular (subfield)
Methods: Evoked potentials, Single-unit activity, calcium imaging, Smoothing, state filtering, decompositions
Keywords: Neural circuits, Fluorescence imaging
MeSH: Behavior, Animal*, Caenorhabditis elegans*, Animals, Axons, Calcium, Interneurons, Microscopy, Fluorescence, Muscles, Sensory Receptor Cells (* major topic)
Topic: Genetics, Aging, and Longevity in Model Organisms (Aging, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: Canadian Institutes of Health Research (PJT-155980); Natural Sciences and Engineering Research Council of Canada (RGPIN-2020-04928, PGS/D-579692)
Citations: cited by 3 papers (Europe PMC); 38 references in the paper

Abstract

Understanding the neural basis of behavior requires imaging cellular activity in freely moving animals, which typically demands expensive, restrictive microscopy setups. To overcome these barriers, we developed Wormspy, a cost-effective, open-source epifluorescence microscopy system for high-magnification imaging and tracking of Caenorhabditis elegans. Wormspy enables the simultaneous recording of neuronal activity and behavioral dynamics without needing the animal to be restrained. We demonstrate its utility in imaging body wall muscles, sensory neurons, and subcellular calcium events within interneuron axons. Our platform reproduces known mutant phenotypes and uncovers, to the best of our knowledge, previously inaccessible sensorimotor correlations. We show that Wormspy provides a robust, modular framework that lowers technical barriers to high-resolution neural imaging, enabling flexible experimental designs for dissecting behavior in freely moving organisms.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repositories

Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.

Zenodo 19477903

License: CC-BY-4.0
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: “Data availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: NumPy (14 files), OpenCV (8 files), pandas (8 files), tifffile (7 files), Matplotlib (6 files), Pillow (5 files), imageio (3 files), PyTorch (2 files), scikit-image (2 files), SciPy (2 files), h5py (1 file), seaborn (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
  • 28 September 2026: the link answers (HTTP 200)
19 files
At the source:

Hendricks-Worm-Lab/WormsPy_paper_analysis

License: none: the authors keep all their rights
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Commit: 39a954adc94ac157adb4aa95d4dcefbc9e20ddc2, 19 April 2026
Languages: Python (17), Jupyter (1)
Size: 138 files, 18 scripts
Software Heritage: not archived
Found in: “Code availability”
Holds: README, 1 notebook
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: NumPy (14 files), OpenCV (8 files), pandas (8 files), tifffile (7 files), Matplotlib (6 files), Pillow (5 files), imageio (3 files), PyTorch (2 files), scikit-image (2 files), SciPy (2 files), h5py (1 file), seaborn (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers
  • 28 September 2026: the link answers
19 files
At the source: github.com/Hendricks-Worm-Lab/WormsPy_paper_analysis

sebzdead.github.io/wormspy

License: none: the authors keep all their rights
State: the link answers, verified on 28 September 2026
Evidence: the link answers
Software Heritage: not checked
Found in: “Code availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
  • 28 September 2026: the link answers (HTTP 200)
At the source: sebzdead.github.io/WormsPy/

Zenodo 19477899

License: CC-BY-4.0
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: the references
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: NumPy (3 files), OpenCV (3 files), tifffile (3 files), imageio (2 files), scikit-image (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
  • 28 September 2026: the link answers (HTTP 200)
3 files
At the source:

Zenodo 19477902

License: CC-BY-4.0
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: the references
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: NumPy (14 files), OpenCV (8 files), pandas (8 files), tifffile (7 files), Matplotlib (6 files), Pillow (5 files), imageio (3 files), PyTorch (2 files), scikit-image (2 files), SciPy (2 files), h5py (1 file), seaborn (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
  • 28 September 2026: the link answers (HTTP 200)
19 files
At the source:

hendricks-worm-lab/gcamp_analysis

License: none: the authors keep all their rights
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Commit: 72361f7742283e511379ec4b830727dc83a42c6a, 1 March 2024
Languages: Python (3)
Size: 3 files, 3 scripts
Software Heritage: not archived
Found in: the Zenodo archive record
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: NumPy (3 files), OpenCV (3 files), tifffile (3 files), imageio (2 files), scikit-image (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers
  • 28 September 2026: the link answers
3 files
At the source: github.com/Hendricks-Worm-Lab/GCaMP_analysis/tree/V1.0

Code availability

https://github.com/Hendricks-Worm-Lab/WormsPy_paper_analysis. The custom software package used for microscope control and tracking (Wormspy) is available on GitHub https://sebzdead.github.io/WormsPy/37. The custom segmentation and analysis code is available on GitHub38.

Reproduced under the paper's license (CC BY), from the paper cited above.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 6 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 60 scripts, each with its path and the digest of its content;
  • 2 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data availability

The data generated in this study are accessible at 10.5281/zenodo.19477903. Source data are provided with this paper.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 5 authors, 2 keywords, 9 MeSH terms, 2 funders, 37 references.

Cite

This paper

Wittekindt, S. N., Owens, H., Guisnet, A., Wittekindt, L., & Hendricks, M. (2026). An epifluorescence microscope design for naturalistic behavior and cellular activity in freely moving Caenorhabditis elegans. Nature communications, 17(1), 4411. https://doi.org/10.1038/s41467-026-72709-w

BibTeX

@article{wittekindt2026epifluorescence,
author = {Wittekindt, Sebastian N. and Owens, Hannah and Guisnet, Aurélie and Wittekindt, Lennard and Hendricks, Michael},
title = {{An epifluorescence microscope design for naturalistic behavior and cellular activity in freely moving Caenorhabditis elegans}},
journal = {Nature communications},
year = {2026},
month = may,
volume = {17},
number = {1},
pages = {4411},
publisher = {Nature Publishing Group},
issn = {2041-1723},
doi = {10.1038/s41467-026-72709-w},
url = {https://doi.org/10.1038/s41467-026-72709-w},
pmid = {42156741},
pmcid = {PMC13187321}
}

RIS

TY - JOUR
AU - Wittekindt, Sebastian N.
AU - Owens, Hannah
AU - Guisnet, Aurélie
AU - Wittekindt, Lennard
AU - Hendricks, Michael
TI - An epifluorescence microscope design for naturalistic behavior and cellular activity in freely moving Caenorhabditis elegans
T2 - Nature communications
J2 - Nat Commun
PY - 2026
DA - 2026/05/19
VL - 17
IS - 1
SP - 4411
SN - 2041-1723
PB - Nature Publishing Group
DO - 10.1038/s41467-026-72709-w
UR - https://doi.org/10.1038/s41467-026-72709-w
LA - en
ER -

CSL-JSON

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"title": "An epifluorescence microscope design for naturalistic behavior and cellular activity in freely moving Caenorhabditis elegans",
"container-title": "Nature communications",
"author": [
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"family": "Wittekindt",
"given": "Sebastian N."
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