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)

Installation

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-interface
- element-interface contains data loading utilities for element-calcium-imaging.
- element-interface 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-interface 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-interface.
- Install element-interface with scanreader
```
pip install "element-interface[scanreader] @ git+https://github.com/datajoint/element-interface"
```
- Install element-interface with sbxreader
```
pip install "element-interface[sbxreader] @ git+https://github.com/datajoint/element-interface"
```
- Install element-interface with Suite2p
```
pip install "element-interface[suite2p] @ git+https://github.com/datajoint/element-interface"
```
- Install element-interface with CaImAn requires two separate commands
```
pip install "element-interface[caiman_requirements] @ git+https://github.com/datajoint/element-interface"
pip install "element-interface[caiman] @ git+https://github.com/datajoint/element-interface"
```
- Install element-interface with multiple packages
```
pip install "element-interface[caiman_requirements] @ git+https://github.com/datajoint/element-interface"
pip install "element-interface[scanreader,sbxreader,suite2p,caiman] @ git+https://github.com/datajoint/element-interface"
```

Element usage

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

GeetikaSi/element-calcium-imaging