Introduction

CICADA stands for Calcium Imaging Complete Automated Data Analysis.

It’s a Python pipeline aimed for analyzing calcium imaging data.

Motivation

We notice a lack of toolboxes or analysis pipelines for calcium imaging data, using open source language. Our motivation was to build an easy-to-use pipeline, which doesn’t need programming skills. In that purpose, we offer a Graphical User Interface as well as a command line usage.

In order to tackle the broadness of scientists’ needs, we built the pipeline to be easily extendable with a plugin-like interface, for data format and analyses.

Supported data format

The default data format chosen was Neurodata Without Borders: Neurophysiology (NWB:N). that is a data standard for neurophysiology, providing neuroscientists with a common standard to share, archive, use, and build analysis tools for neurophysiology data. NWB:N is designed to store a variety of neurophysiology data, including data from intracellular and extracellular electrophysiology experiments, data from optical physiology experiments, and tracking and stimulus data.

We provide some tools to convert their data into NWB, with a plugin-like interface. (Curently in Preprocessing)

Functionalities

  • We offer a Graphical User Interface (GUI) as well as a command line usage.

  • We have already implemented or aim to implement various kind of analyses such cell assemblies detection, network analyses, display functions (rasters, cells map) etc…

  • The GUI offers specifics functionalities:

    • Subjects and recorded sessions can be filtered or grouped in order to easily select the data to be analysed, and saved for future use.

    • Subjects and and recorded sessions’ informations can be displayed and modified depending on the data format.

    • Analyses are grouped by family. Each analysis provide a way to check the data see if they are compatible.

    • Analyses arguments can be saved in a yaml file allowing to easily load them later.

    • A multi-thread implementation allows multiple analysis at the same time.

    • A progression bar allows to follow the analysis current status.