element-miniscope 0.1.2

Miniscope DataJoint Element

DataJoint Element - Miniscope Calcium Imaging

• This repository features a DataJoint pipeline design for functional calcium imaging data acquired with the UCLA Miniscope and Miniscope DAQ V4 acquisition system, and analyzed with CaImAn.

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

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

• See the Element Miniscope 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

• As the diagram depicts, elements-miniscope starts immediately downstream from Session, and also requires some notion of:

  • Equipment for equipment/device

  • AnatomicalLocation as a dependency for RecordingLocation

Table definitions

The miniscope schema contains all tables in this Element, including for the acquired metadata and analysis results.

Recording

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• A Session (more specifically an experimental session) may have multiple recordings, where each recording describes a complete 3D dataset (i.e. 2d image over time) from one recording session, typically from the moment of pressing the start button to pressing the stop button.

• Recording - table containing information about the equipment used (e.g. the acquisition hardware information)

• RecordingInfo - metadata about this recording from the Miniscope DAQ software (e.g. frame rate, number of channels, frames, etc.)

Motion correction

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• MotionCorrection - motion correction information performed on a recording

• MotionCorrection.RigidMotionCorrection - details of the rigid motion correction (e.g. shifting in x, y)

• MotionCorrection.NonRigidMotionCorrection and MotionCorrection.Block tables are used to describe the non-rigid motion correction.

• MotionCorrection.Summary - summary images after motion correction (e.g. average image, correlation image, etc.)

Segmentation

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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

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

Neural activity extraction

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• Fluorescence - fluorescence traces extracted from each Segmentation.Mask

• ActivityExtractionMethod - activity extraction method (e.g. deconvolution) applied on the 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-miniscope

  pip install element-miniscope
  

• Install element-interface

  • element-interface contains data loading utilities for element-miniscope.

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

    install "element-interface @ git+https://github.com/datajoint/element-interface"
    

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

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

Usage

Element activation

When using this Element, one needs to run miniscope.activate to declare the schemas and tables on the database.

Click to expand details

To activate element-miniscope, ones need to provide:

1. Schema names

   • schema name for the miniscope module

2. Upstream tables

   • Session table: A set of keys identifying a recording session (see Element-Session).
   • Equipment table: A reference table for Recording, specifying the equipment used for the acquisition (see example pipeline).
   • AnatomicalLocation table: A reference table for RecordingLocation, specifying the brain location where the recording is acquired

3. Utility functions. See example definitions here.

   • get_miniscope_root_data_dir(): Returns your root data directory.
   • get_session_directory(): Returns the path of the session data relative to the root directory.

For more details, check the docstring of element-miniscope:

    help(miniscope.activate)

Element usage

• See the workflow-miniscope repository for an example usage of element-miniscope.

• Our YouTube tutorial walks through all the key details of this Element.

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 Miniscope (version <Enter version number>)