element-calcium-imaging 0.2.2

Calcium Imaging DataJoint element

DataJoint Element - Functional Calcium Imaging

• This repository features DataJoint pipeline design for functional Calcium imaging with ScanImage, Scanbox, or Nikon NIS 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 the Element Calcium Imaging documentation for the background information and development timeline.

• For more information on the DataJoint Elements project, please visit https://elements.datajoint.org. This work is supported by the National Institutes of Health.

Element architecture

element-calcium-imaging is comprised of two schemas, scan and imaging. To handle several use cases of this pipeline, we have designed several imaging schemas, including imaging, imaging_no_curation, and imaging_preprocess.

• imaging - Multiple scans are acquired during each session and each scan is processed independently.

• imaging_preprocess - Multiple scans are acquired during each session and each scan is processed independently. And pre-processing steps can be performed on each scan prior to processing with Suite2p or CaImAn.

imaging module

imaging_preprocess module

• 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

Table definitions

Scan

The scan schema contains information regarding the raw data acquired with ScanImage or Scanbox.

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• 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

The imaging schema stores information regarding the motion corrected images.

Click to expand details

• 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

The imaging schema stores information regarding the segmented masks for each field.

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• 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

The imaging schema stores information regarding the calcium traces for each mask.

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• 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

• The installation instructions can be found at the DataJoint Elements documentation.

• 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.

  Click to expand details

  • 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.

Citation

• If your work uses DataJoint and DataJoint Elements, please cite the respective Research Resource Identifiers (RRIDs) and manuscripts.

• DataJoint for Python or MATLAB

  • Yatsenko D, Reimer J, Ecker AS, Walker EY, Sinz F, Berens P, Hoenselaar A, Cotton RJ, Siapas AS, Tolias AS. DataJoint: managing big scientific data using MATLAB or Python. bioRxiv. 2015 Jan 1:031658. doi: https://doi.org/10.1101/031658

  • DataJoint (RRID:SCR_014543) - DataJoint for <Select Python or MATLAB> (version <Enter version number>)

• DataJoint Elements

  • Yatsenko D, Nguyen T, Shen S, Gunalan K, Turner CA, Guzman R, Sasaki M, Sitonic D, Reimer J, Walker EY, Tolias AS. DataJoint Elements: Data Workflows for Neurophysiology. bioRxiv. 2021 Jan 1. doi: https://doi.org/10.1101/2021.03.30.437358

  • DataJoint Elements (RRID:SCR_021894) - Element Calcium Imaging (version <Enter version number>)