aqua-py-analysis

Analysis codebase for paper: Ca+ activity maps of astrocytes tagged by axoastrocytic AAV transfer

Requirements:

• Python 3.7

Additional requirements for AquA preprocessing:

• Matlab 2019a+

Datasets

Dataset available here
Dataset structure	Dataset file structure
First astrocyte experiment dataset	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
Second astrocyte experiment dataset	Used to assess if multiple vibrissa stimuli alter calcium activity in astrocytes in relation to single vibrissae stimuli/no stimuli)
Astro-axon dataset	Axon and astrocyte calcium activity during behavioural and vibrissa stimulation
Data plots curation SA	Plots as presented in paper sorted by Figure
Data plots	All relevant generated plots

Loading datasets

Notebooks
AstrocyteExample.ipynb	Astrocyte notebook example of dataset loading
AxonAstrocyteExample.ipynb	Axon-Astro notebook example of dataset loading
Paper related notebooks
generate_astrocyte_paper_plots.ipynb	Generates relevant paper plots from first/second astrocyte experiment dataset
generate_axon_paper_plots.ipynb	Generates relevant paper plots from astro-axon 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

Preprocessing (creating your own dataset)

See preprocessing-README for details

Important note

The objective of this github repository is to replicate the analysis of AquA processed data generated for this paper. Although the codebase can be used for new experiments, it might have to be modified to account for different experimental conditions.