Dataset DOI: 10.5061/dryad.v15dv4291

Description of the data and file structure

This dataset constitutes the second part of the complete dataset containing data and code required to replicate analyses in Saiseau, Busson, and Durand (submitted, see preprint https://doi.org/10.48550/arXiv.2501.02651). It was collected to characterise slow, system-scale modulations of contractile activity in the slime mould Physarum polycephalum confined in annular (ring) chambers. Plasmodia were grown on aqueous agar substrates (5 with/ 11 without nutrients) and then shaped into concentric annular specimens by pressing thin cylindrical walls into the gel; ring perimeters in this dataset range from 6.0 to 13.5 cm (aspect ratios =1141).

We recorded 47 ring experiments obtained from 16 individual specimens. Time-lapse transmitted-light imaging (blue channel) was used to capture thickness/optical-intensity dynamics; typical acquisition intervals were 46 s and individual recordings lasted 412 hours. Experiments were performed under controlled laboratory conditions (dark chamber, T=25 C). From the raw image stacks we provide segmentation masks, ring geometry parameters, and extracted angular-sector time series of a thickness proxy (mean and standard deviation per sector). We also include processed data: amplitude/phase/drift decompositions, concatenated in an analysis file (Contractile_rings_data.pick), and the Python scripts used for segmentation, extraction and analysis. These data support the manuscript results: identification of an intrinsic modulation period, classification of slow spatio-temporal modes (rotating vs alternating), scaling of rotating-mode periods with system size, and statistical evidence consistent with transport-mediated coordination via a slowly advected regulator.

Details of the preparation, experimental protocol, and data processing/analysis, can be found in supplementary materials file.

Files and variables

File: Specimen14.zip

Description: Raw image time series of specimen S14 (transmitted-light stacks; Basler Camera; 16-bit TIFF; dt = 4 seconds)

File: Contractile_rings_data.pick

Description: Concatenated Python pickle containing angular-sector time series of thickness-derived variables (phase, amplitude, drift), metadata, for a total of 15 features across the 47 ring experiments. Fields include:
['ID', 'imgpath','dt', 'rayon', 'périmètre', 'largeur', 'amplitude', 'dérive', 'phase', 'vitesse', 'fréquence', 'MP_vitesse', 'MP_fréquence', 'durée manip', 'nspb'']

• ID : unique identifier for the ring experiment.
• imgpath : storage location in the local repository (not applicable here).
• dt : acquisition time step (seconds).
• rayon : ring main-axis radius (units as recorded; see rings_data).
• périmètre: ring perimeter L (same length units as rayon).
• largeur : ring thickness e (annulus width).
• amplitude : amplitude envelope A(,t) per-sector time series (array).
• dérive: height drift signal D(,t) per-sector time series (array).
• phase : instantaneous phase (,t)\phi(\theta,t)(,t) per-sector time series (array), typically unwrapped or wrapped depending on processing step.
• vitesse : transport/rotation speed estimates computed from isophase slopes.
• fréquence : local instantaneous or dominant frequency (Hz) derived from phase time derivative.
• MP_vitesse, MP_fréquence : most-probable (mode) transport speed and frequency.
• durée manip : duration of the recording (frames).
• nspb: number of angular sectors.

File: Scripts_Figures.zip

Description: Archive of the Python analysis and plotting scripts, Figures data, and figure-generation code used to reproduce every manuscript figure (dependencies listed in script headers).

File: Figures.zip

Description: Archive containing all final manuscript figures in high-resolution formats.

File: Supplementary_Figures.zip

Description: Archive containing all added supplementary figures in high-resolution formats.

File: Specimen15.zip

Description: Raw image time series of specimen S15 (transmitted-light stacks; Basler Camera; 16-bit TIFF; dt = 4 seconds)

File: Specimen19.zip

Description: Raw image time series of specimen S19 (transmitted-light stacks; Basler Camera; 16-bit TIFF; dt = 4 seconds)

File: Specimen16.zip

Description: Raw image time series of specimen S16 (transmitted-light stacks; Basler Camera; 16-bit TIFF; dt = 4 seconds)

File: Rings_parameters.zip

Description: Scripts for ring segmentation and per-sector height extraction, a custom function library, and per-specimen parameter files (general_params) together with per-ring parameter and outputs (rings_data, rings_masks, I_diag, I_std).

File: Image_processing.zip

Description: Scripts to process time-lapse microscopy image series of ring-confined plasmodia (e.g. Physarum polycephalum) and extract dynamical signals from annular regions.

File: physarum-ring-modes-Analysis.zip

Description: This repository accompanies the quantitative study of slow spatio-temporal modulation of contractile activity in ring-confined Physarum polycephalum plasmodia. It contains:
- Raw kymograph data — one pickle file (Contractile_rings_data.pick) holding pre-processed thickness signals for all 47 ring experiments (total recording: 482 h).
- Pre-computed result tables — five CSV files in results/, produced by the pipeline and ready to use without re-running.
- Analysis pipeline — Python scripts in scripts/ that detect slow-modulation episodes from the pickle and write the result tables.
- Figure scripts — Python scripts in Figure scripts/ that read the result tables or the pickle and reproduce every figure in the paper and supplementary.

File: Files_list_Nutrients.xlsx

Description: Table separating specimen grown on gels with/without added oatmeal

File: Supplementary__2026_Physarum_Modulation.pdf

Description: Supplementary material detailing experimental methods, data-processing parameters, algorithm descriptions, and additional figures supporting the main text.

Code/software

Analysis codes are provided in Python. Required Python libraries are documented in the header of the scripts provided. Typical dependencies include numpy, scipy, matplotlib, pandas and image-processing libraries; exact versions are recorded in the script headers. The code comments list the necessary libraries and any non-standard requirements.

1. Inspect the general_params.j file in the specimen folder to find the image paths and acquisition dt.

2. Use the scripts in Rings_parameters to reproduce segmentation masks if needed.

3. The extracted height dynamics per angular sector are provided in I_diag and I_std, and the full concatenated file Contractile_rings_data.pick is the starting point for the analysis scripts in Scripts_Figures.

4. See the header comments of each analysis script for exact call arguments and plotting options.

Access information

Other publicly accessible locations of the data:

• (first part) 10.5061/dryad.2z34tmq08
• part of the data are available here https://doi.org/10.17605/OSF.IO/DP58G