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Calc Cobra (TODO) is a data pipeline for processing and analysing task-specific (widefield) calcium imaging data through neural decoding. Here, calcium activity is a proxy for neuronal activations. It provides stand-alone functionalities to visualize the data as well as enabling the export of processed data for other visualization purposes.

Feature Overview

• Brain Alignment (between different Sessions and Subjects)
  • Automatic Registration with novel MesoNet (under development)
• Different data-driven & anatomical parcellations
  • Including novel locaNMF to obtain interpretable, data-driven brain sub-regions
• Different brain connectivity measurements
  • Functional connectivity (statistical relationship)
  • Effective connectivity (est. causal influence)
    • Novel MOU-EC fits generative network model

Installation

• Required Software

  • Python >= 3.8
  • Anaconda
  • Snakemake

• Required Files

  • Put the experimental data into resources/experiment/mouse-id/experiment-date/ with mouse-id and experiment-date being provided by you
    • e.g. ../repository/resources/experiment/GN06/2021-01-20_10-15-16

• Trouble Shooting

  • To use Virtual Environment with Anaconda on Windows you may need to:
    • download the buidling wheels for tables und h5py from here
    • installing through pip leads to errors in other modules

Usage

• Commands
• Config

• Results

Development

• File Structure

• Pipeline Steps

  • Loading & Preprocessing
  • Parcellation
  • Filtering
  • Condition Extraction
  • Feature Calculation
  • Recursive Feature Elimination
  • Deconding
  • Plotting