Metadata-Version: 2.1
Name: element-calcium-imaging
Version: 0.1.0b0
Summary: Calcium Imaging DataJoint element
Home-page: https://github.com/datajoint/element-calcium-imaging
Author: DataJoint NEURO
Author-email: info@vathes.com
License: MIT
Description: # 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](Background.md) for the background information and development timeline.
        
        ## Element architecture
        
        ![element-calcium-imaging diagram](images/attached_calcium_imaging_element.svg)
        
        + 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
        
        ```
        pip install element-calcium-imaging
        ```
        
        If you already have an older version of ***element-calcium-imaging*** installed using `pip`, upgrade with
        ```
        pip install --upgrade element-calcium-imaging
        ```
            
            
        A separate dependency is required: [***scanreader***](https://github.com/atlab/scanreader), to install:
        ```
        pip install git+https://github.com/atlab/scanreader.git
        ```
        
        ## Element usage
        
        + See [workflow-calcium-imaging](https://github.com/datajoint/workflow-calcium-imaging) 
        repository for an example usage of `element-calcium-imaging`.
        
        
            
Keywords: neuroscience calcium-imaging science datajoint
Platform: UNKNOWN
Description-Content-Type: text/markdown
