DOI: 10.5281/zenodo.13683455
title: Photomovement of Euglena and Volvox in the DOME

description: Photomovement of Microorganisms in the DOME

Intro

This dataset presents experimental data on the movement and light response of two species of microorganisms, specifically Euglena gracilis and Volvox aureus.

Experiments were performed using the experimental platform DOME. A water sample containing multiple specimens of microorganisms was imaged with a microscopic camera. Simultaneously, light inputs, either time-varying or spatially defined, were projected onto the sample. Automatic object detection and tracking were employed to capture the trajectories and spatial distribution of the microorganisms. This data, together with the known light inputs, enables the study of the microorganisms’ light responses, detailing both individual behaviors (e.g., photokinesis) and collective behaviors (e.g., photoaccumulation).

The related work on modelling the photomovement of microorganisms, with additional details on data acquisition and elaboration, is presented in Giusti et al., "Data-driven inference of digital twins for high-throughput phenotyping of motile and light-responsive microorganisms", Journal of the Royal Society Interface, 2026.

The Python software used to control the DOME, run experiments, atomatically track the movement of microorganisms and generate these data is available at DOME-software (code_DOME-software.zip contains the version used for these data).

The Matlab software to further analyze these data, generate digital twins of the microorganisms and run virtual experiments is available at SwarmSim (code_SwarmSim.zip contains the version used for these data).

Content description

Each SPECIES_SCENARIO.zip file contains data from a specific experimental scenario, including multiple replicates and/or aggregated data.

In the following M represents the number of sampling instants occurred during an experiment, and N the number of agents observed.

Scenarios with time-varying inputs

Files from scenarios with time-varying inputs have the following structure:

SPECIES_SCENARIO.zip|- DATE_SPECIES_1                            Folder of a single experiment (i.e. replicate).|  |- data.npz                                   Experimental data and parameters. Compressed numpy file with the following fields:|  |  |  |> activation_times    Sampling time instants. Size M. Units [s].|  |  |  |> totalT                          Total duration of the experiment. Units [s].|  |  |  |> deltaT                          Nominal sampling time step. Units [s].|  |  |  |> commands                     Input commands applied during the experiment. List of dictionaries.|  |  |  |> camera2projector   Linear transformation matrix between camera and projector frames. Size 3x3.|  |  |  |> off_light                   Light value correspondig to zero input. BGR values.|  |  |  |> on_light                     Light value correspondig to full input. BGR values.|  |- experiment_log.txt            Experimental parameters and log. Human readable.|  |- images                                       Folder of pictures acquired during the experiment.|  |- patterns                                   Folder of input patterns as projected by the projector.|  |- patterns_cam                          Folder of input patterns as seen by the camera.|  |- tracking_DATE                        Folder of data generated during tracking and data processing.|  |  |- analysis_data.npz        Data from tracking procedure. Compressed numpy file with the following fields:|  |  |  |> positions                   Position of agents in the camera frame at each time instant. Size MxNx2. Units [px].|  |  |  |> inactivity                 Inactivity counter of agents at each time instant. Size MxN.|  |  |  |> total_cost                 Total tracking cost.|  |  |  |> parameters                 Tracking parameters.|  |  |- analysed_data.npz        Processed trajectories data. Compressed numpy file with the following fields:|  |  |  |> time_steps                 Duration of the sampling time steps. Size M-1. Units [s].|  |  |  |> interp_positions    Smoothed and interpolated positions of the agents. Size MxNx2. Units [px].|  |  |  |> speeds_smooth           Smoothed longitudinal speeds of the agents. Size MxN. Units [um/s].|  |  |  |> ang_vel_smooth         Smoothed angular speeds of the agents. Size MxN. Units [rad/s].|  |  |  |> inputs                          Sequence of light inputs (averaged over space). Size Mx3. BGR values.|  |  |- inputs.txt                        Light inputs. Tab-separeted file. BGR format with 0-255 range.|  |  |- ang_vel_smooth.txt      Recorded angular velocity of the microorganisms. Tab-separeted file. Units [rad/s].|  |  |- speeds_smooth.txt        Recorded speed of the microorganisms. Tab-separeted file. Units [um/s].|  |  |- plots                                   Folder of images from data analysis.|  |  |- tracking.mp4                   Video with microorgnisms tracking.|  |  |- trk_00.0.jpeg                 Image of microorgnisms tracking at time instant 0s.|  |  |...|  |  |- trk_180.0.jpeg              Image of microorgnisms tracking at time instant 180s.|... |- DATE_SPECIES_N                            Folder of a single experiment (i.e. replicate).|- combo                                                Folder of combined data from multiple replicates. |  |- combo_info.txt                     Description of combined data from multiple replicates. Human readable.|  |- inputs.txt                              Light inputs. Tab-separeted file. BGR format with 0-255 range.|  |- ang_vel_smooth.txt            Recorded angular velocity of the microorganisms. Tab-separeted file. Units [rad/s].|  |- speeds_smooth.txt              Recorded speed of the microorganisms. Tab-separeted file. Units [um/s].|  |- plots                                         Folder of images from data analysis.

Scenarios with spatial inputs

Files from scenarios with spatial inputs have the following structure:

SPECIES_SCENARIO.zip|- DATE_SPECIES_1                            Folder of a single experiment (i.e. replicate).|  |- data.npz                                   Experimental data and parameters. Compressed numpy file. See above for information about the fields.|  |- experiment_log.txt            Experimental parameters and log. Human readable.|  |- images                                       Folder of pictures acquired during the experiment.|  |- patterns                                   Folder of input patterns as projected by the projector.|  |- patterns_cam                          Folder of input patterns as seen by the camera.|  |- background.jpeg                   Background image generated by the tracking software.|... |- DATE_SPECIES_N                            Folder of a single experiment (i.e. replicate).