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Concepts

Multiphoton Calcium Imaging

Over the past two decades, in vivo two-photon laser-scanning imaging of calcium signals has evolved into a mainstream modality for neurophysiology experiments to record population activity in intact neural circuits. The tools for signal acquisition and analysis continue to evolve but common patterns and elements of standardization have emerged.

The preprocessing pipeline for two-photon laser-scanning microscopy includes motion correction (rigid or non-rigid), cell segmentation, and calcium event extraction (sometimes described as "deconvolution" or "spike inference"). Some include raster artifact correction, cropping and stitching operations.

Raw Scans Motion Corrected Scans Cell Segmentation Calcium Events

Left to right: Raw scans, Motion corrected scans, Cell segmentation, Calcium events

For a long time, most labs developed custom processing pipelines, sharing them with others as academic open-source projects. This has changed recently with the emerging of a few leaders as the standardization candidates for the initial preprocessing.

  • CaImAn (Originally developed by Andrea Giovannucci, current support by FlatIron Institute: Eftychios A. Pnevmatikakis, Johannes Friedrich)
  • Suite2p (Carsen Stringer and Marius Pachitariu at Janelia), 200+ users, active support
  • EXTRACT (Hakan Inan et al. 2017, 2021).

Element Calcium Imaging encapsulates these packages to ease the management of data and its analysis.

Acquisition tools

Hardware

The primary acquisition systems are:

  • Sutter
  • Thorlabs
  • Bruker
  • Neurolabware

We do not include Miniscopes in these estimates. In, all there are perhaps on the order of 3000 two-photon setups globally but their processing needs may need to be further segmented.

Software

  • Vidrio ScanImage
  • Thorlabs ThorImageLS
  • Scanbox
  • Nikon NIS-Elements
  • Bruker Prairie View

Data Export and Publishing

Element Calcium Imaging supports exporting of all data into standard Neurodata Without Borders (NWB) files. This makes it easy to share files with collaborators and publish results on DANDI Archive. NWB, as an organization, is dedicated to standardizing data formats and maximizing interoperability across tools for neurophysiology.

To use the export functionality with additional related dependencies, install the Element with the nwb option as follows:

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pip install element-calcium-imaging[nwb]