Paper title: Ca2+ activity maps of astrocytes tagged by axo-astrocytic AAV transfer Authors: Georgiou Leonidas, Echeverría Anaí, Georgiou Achilleas, Kuhn Bernd Institution: Okinawa Institute of Science and Technology --------------------------------------------- --------------------------------------------- Abstract: The dataset contains 5 files: 1) astro_first_experiment.zip - Main dataset. Used to assess spatiotemporal organisation of astrocyte calcium signals during different behavioural states - rest, run, vibrissa stimulation, vibrissa exploration, and to generate the activity heatmaps 2) astro_second_experiment.zip - Supplementary dataset. Used to assess if multiple vibrissa stimuli alter calcium activity in astrocytes in relation to single vibrissae stimuli/no stimuli) 3) astro_axons.zip - Supplementary dataset. Axon and astrocyte calcium activity during behavioural and vibrissa stimulation 4) aqua-py-analysis.zip - Library used to analyse all data 5) Data_curation_SA.zip - A summary of data plots and tables generated and used for the paper - Note: figure 1 was split into 2 figures for editorial reasons. Here figure 1 and 2 are grouped as figure 1. - For more extensive documentation please refer to: https://github.com/Achilleas/aqua-py-analysis - For the experimental methodology used in each experiment please see Methods section in Dryad and the paper - Main requirements: - Python 3.7 - Matlab 2019a+ (only for preprocessing with AQuA, not required for inspecting existing results) --------------------------------------------- --------------------------------------------- Data structure (main and supplementary datasets): astro_first_experiment.zip --------------------------------------------- | |- astrocyte_id | |- day_i The day of the astrocyte recording | |- aqua_bound/aqua_merged Aqua results run with cell boundaries (only events inside cell included) |- aqua_no_bound/aqua_merged Aqua results run without cell boundaries |- oscilloscope Oscilloscope data - movement of treadmill = speed |- roi_data Region of interest (ROI) raw data (whisker, stick, pupil (unused)) |- roi_data_merged roi_data in more compact form |- sample May include supplementary tiff file video --------------------------------------------- astro_second_experiment.zip --------------------------------------------- | | - astrocyte_id_experiment_id | - day_i The day of the astrocyte recording | | - aqua_bound/aqua_merged Aqua results run with cell boundaries (only events inside cell included) | - oscilloscope Oscilloscope data - movement of treadmill = speed | - reference-images reference images for registration | - roi_data Region of interest (ROI) raw data (whisker, stick, pupil (unused)) | - roi_data_merged roi_data in more compact form | - rois.zip | - Experiment_info.txt Supplementary experiment info --------------------------------------------- astro_axons.zip --------------------------------------------- | | - astrocyte_id | | - day_i | | - aqua_no_bound/aqua_merged Aqua results run without cell boundaries | - axon_astro_landmarks Landmarks chosen for astrocytes/axons in video | - axon_only_bound | - oscilloscope Oscilloscope data - movement of treadmill = speed | - roi_data_merged roi_data in more compact form | - sample Samples --------------------------------------------- --------------------------------------------- Analysis information (GitHub repository/aqua-py-analysis.zip) --------------------------------------------- - For all analysis information preferably refer to: https://github.com/Achilleas/aqua-py-analysis - In brief the GitHub repository above contains the following: - Datasets (the datasets used in the paper and described in the abstract): - Dataset structure - Notebook summarising dataset file structure - First astrocyte experiment dataset - Main dataset - Second astrocyte experiment dataset - Supplementary dataset - Astro-axon dataset - Supplementary dataset - Data plots curation SA - Plots as presented in paper sorted by Figure - Plots - All relevant generated plots --------------------------------------------- - Loading datasets (here you will find a list of notebooks on how to load, plot and analyse the datasets) - AstrocyteExample.ipynb - A notebook example on loading the astro datasets - AxonAstrocyteExample.ipynb - A notebook example on loading the astro_axons dataset - generate_astrocyte_paper_plots.ipynb - Generates relevant paper plots from first (main) and second (supplementary) astrocyte experiment datasets - generate_axon_paper_plots.ipynb - Generates relevant paper plots from astro-axon (supplementary) experiment dataset - generate_misc_paper_plots.ipynb - Generates other remaining paper plots (capsid density plot, astrocyte density plot in different cortical layers, neuron density plot in different cortical layers) - statistical_analysis.ipynb - Statistical analysis of datasets generated relevant to paper --------------------------------------------- --------------------------------------------- Other important files (also found in https://github.com/Achilleas/aqua-py-analysis): - preprocessing-README - A useful guide on how to prepossess the raw data - requirements.txt - A list of python libraries used in the analysis --------------------------------------------- --------------------------------------------- ---------------------------------------------