This repository features DataJoint pipeline design for functional Calcium imaging, with ScanImage or Scanbox acquisition system and Suite2p or CaImAn suites for analysis.

The element presented here is not a complete workflow by itself, but rather a modular design of tables and dependencies specific to the functional Calcium imaging workflow.

This modular element can be flexibly attached downstream to any particular design of experiment session, thus assembling a fully functional calcium imaging workflow.

See Background for the background information and development timeline.

• As the diagram depicts, the imaging element starts immediately downstream from Session, and also requires some notion of:

  • Scanner for equipment/device

  • Location as a dependency for ScanLocation

• A Session (more specifically an experimental session) may have multiple scans, where each scan describes a complete 4D dataset (i.e. 3D volume over time) from one scanning session, typically from the moment of pressing the start button to pressing the stop button.

• Scan - table containing information about the equipment used (e.g. the Scanner information)

• ScanInfo - meta information about this scan, from ScanImage header (e.g. frame rate, number of channels, scanning depths, frames, etc.)

• ScanInfo.Field - a field is a 2D image at a particular xy-coordinate and plane (scanning depth) within the field-of-view (FOV) of the scan.

  • For resonant scanner, a field is usually the 2D image occupying the entire FOV from a certain plane (at some depth).

  • For mesoscope scanner, with much wider FOV, there may be multiple fields on one plane.

• MotionCorrection - motion correction information performed on a scan

• MotionCorrection.RigidMotionCorrection - details of the rigid motion correction (e.g. shifting in x, y) at a per ScanInfo.Field level

• MotionCorrection.NonRigidMotionCorrection and MotionCorrection.Block tables are used to describe the non-rigid motion correction performed on each ScanInfo.Field

• MotionCorrection.Summary - summary images for each ScanInfo.Field after motion correction (e.g. average image, correlation image)

• Segmentation - table specifies the segmentation step and its outputs, following the motion correction step.

• Segmentation.Mask - image mask for the segmented region of interest from a particular ScanInfo.Field

• MaskClassification - classification of Segmentation.Mask into different type (e.g. soma, axon, dendrite, artifact, etc.)

• Fluorescence - fluorescence traces extracted from each Segmentation.Mask

• ActivityExtractionMethod - activity extraction method (e.g. deconvolution) to be applied on fluorescence trace

• Activity - computed neuronal activity trace from fluorescence trace (e.g. spikes)

• Install element-calcium-imaging

  pip install element-calcium-imaging
  

• Upgrade element-calcium-imaging previously installed with pip

  pip install --upgrade element-calcium-imaging
  

• Install element-data-loader

  • element-data-loader contains data loading utilities for element-calcium-imaging.

  • element-data-loader is a dependency of element-calcium-imaging, however it is not contained within requirements.txt, therefore, must be installed in addition to the installation of the element-calcium-imaging.

  • element-data-loader can also be used to install packages used for reading acquired data (e.g. scanreader) and running analysis (e.g. CaImAn).

  • If your workflow uses these packages, you should install them when you install element-data-loader.

  • Install element-data-loader with scanreader

    pip install "element-data-loader[scanreader] @ git+https://github.com/datajoint/element-data-loader"
    

  • Install element-data-loader with sbxreader

    pip install "element-data-loader[sbxreader] @ git+https://github.com/datajoint/element-data-loader"
    

  • Install element-data-loader with Suite2p

    pip install "element-data-loader[suite2p] @ git+https://github.com/datajoint/element-data-loader"
    

  • Install element-data-loader with CaImAn requires two separate commands

    pip install "element-data-loader[caiman_requirements] @ git+https://github.com/datajoint/element-data-loader"
    pip install "element-data-loader[caiman] @ git+https://github.com/datajoint/element-data-loader"
    

  • Install element-data-loader with multiple packages

    pip install "element-data-loader[caiman_requirements] @ git+https://github.com/datajoint/element-data-loader"
    pip install "element-data-loader[scanreader,sbxreader,suite2p,caiman] @ git+https://github.com/datajoint/element-data-loader"
    

• See workflow-calcium-imaging repository for an example usage of element-calcium-imaging.