element-calcium-imaging 0.1.0a4

Calcium Imaging DataJoint element

DataJoint Element - Functional Calcium Imaging

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.

Element architecture

• 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

Scan

• 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.

Preprocessing - Motion Correction

• 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)

Preprocessing - Segmentation

• 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.)

Neural activity extraction

• 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)

Element usage

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

Installation

To install this element:

pip install element-calcium-imaging

A separate dependency is required: scanreader, to install:

pip install git+https://github.com/atlab/scanreader.git