Code for paper From neuron to muscle to movement: a complete biomechanical model of Hydra contractile behaviors

• hydramuscle/model/ : biophysical model for simulating calcium dynamics
• hydramuscle/notebooks/ : jupyter notebooks for saving data and generating figures
• hydramuscle/test/ : codes for running the biophysical model under different conditions
• hydramuscle/midline/ : code for extracting midline
• hydramuscle/biomech/ : biomechanical model for transforming stress to movements
• hydramuscle/utils/ : useful wheels
• hydramuscle/dataset/ : relevant data of the paper
  • 2020-09-28-23-41-19-017767.h5 : simulated calcium dynamics data (for Figure 8CDEF)
  • DyWat_Ecto_80X_Snap12d_label.tif : hydra photo for Figure 3B
  • coords_017767_rlx60_100-350.txt : simulated length of the model (for Figure 8G, 100s-350s)
  • coords_017767_rlx60_350-600.txt : simulated length of the model (for Figure 8G, 350s-600s)
  • dual_channel_cycles.mov : dual-channel imaging video for Figure 7
  • lengths_Pre_Bisect_40x_4fps_ex3.csv : measured length of a real hydra (Figure 8G)
  • neural_gcamp_video.avi : neural GCaMP imaging video for extracting stimulation times (for Figure 8AB)