This repository is for Python codes to analyze circadian time siries.

python3: (worked in 3.7.0)
library: check Pipfile for detail

• Install Python
• Donload or git clone this repository
• Run Python script e.g. python3 "xxxx.py"

• Detection of uncoupled circadian rhythms in individual cells of Lemna minor using a dual-color bioluminescence monitoring system
  Emiri Watanabe, Minako Isoda, Tomoaki Muranaka, Shogo Ito, and Tokitaka Oyama
  Plant and Cell Physiology, Volume 62, Issue 5, May 2021, Pages 815–826, https://doi.org/10.1093/pcp/pcab037

  Python file (modules) used in this paper

  • calculate_min_img.py: Used for managing image files captured in dual-color monitoring
  • data_norm and cos_fit in analyser.FFT_nlls: Used for estimating period by Fast Fourier transform–nonlinear least squares (FFT-NLLS)
  • phase_analysis in analyser.peak_analysis: Used for estimating peak time by a local quadratic curve fitting. Parameters were set as follow.
    avg=1, dt=60, p_range=12, f_avg=1, f_range=9, offset=0, time=False, r2_cut=False, min_tau=16, max_tau=32

• An endogenous basis for synchronisation characteristics of the circadian rhythm in proliferating Lemna minor plants Kenya Ueno, Shogo Ito, Tokitaka Oyama New Phytologist, Volume233, Issue5, March 2022, Pages 2203-2215, https://doi.org/10.1111/nph.17925

  Python file (modules) used in this paper

  • img_circadian_analysis in analyser.phase_from_img: Used for rhythmic analysis in the fronds (Fig2, 3). Parameters were set as follow. img_circadian_analysis(folder, avg=3, calc_range=[start, start + 24 * 3, dt=60, offset=offset, save=True, background=background, tau_range=[16, 32])

京都大学 理学研究科 植物学教室 形態統御学分科 時間生物学グループ（小山研）

There is little documentation for this code. Functions not used in the paper may have bugs in their arguments. Ueno plans to improve the code as a hobby. Please contact @kenya_ueno if you have an urgent need for a function.

@article{ueno2022endogenous,
  title={An endogenous basis for synchronisation characteristics of the circadian rhythm in proliferating Lemna minor plants},
  author={Ueno, Kenya and Ito, Shogo and Oyama, Tokitaka},
  journal={New Phytologist},
  volume={233},
  number={5},
  pages={2203--2215},
  year={2022},
  publisher={Wiley Online Library}
}