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.
-
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 forScanLocation
-
-
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.
-
-
MotionCorrection
- motion correction information performed on a scan -
MotionCorrection.RigidMotionCorrection
- details of the rigid motion correction (e.g. shifting in x, y) at a perScanInfo.Field
level -
MotionCorrection.NonRigidMotionCorrection
andMotionCorrection.Block
tables are used to describe the non-rigid motion correction performed on eachScanInfo.Field
-
MotionCorrection.Summary
- summary images for eachScanInfo.Field
after motion correction (e.g. average image, correlation image)
-
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 particularScanInfo.Field
-
MaskClassification
- classification ofSegmentation.Mask
into different type (e.g. soma, axon, dendrite, artifact, etc.)
-
Fluorescence
- fluorescence traces extracted from eachSegmentation.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)
-
Install
element-calcium-imaging
pip install element-calcium-imaging
-
Upgrade
element-calcium-imaging
previously installed withpip
pip install --upgrade element-calcium-imaging
-
Install
element-data-loader
-
element-data-loader
contains data loading utilities forelement-calcium-imaging
. -
element-data-loader
is a dependency ofelement-calcium-imaging
, however it is not contained withinrequirements.txt
, therefore, must be installed in addition to the installation of theelement-calcium-imaging
. -
element-data-loader
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-data-loader
. -
Install
element-data-loader
withscanreader
pip install "element-data-loader[scanreader] @ git+https://github.com/datajoint/element-data-loader"
-
Install
element-data-loader
withsbxreader
pip install "element-data-loader[sbxreader] @ git+https://github.com/datajoint/element-data-loader"
-
Install
element-data-loader
withSuite2p
pip install "element-data-loader[suite2p] @ git+https://github.com/datajoint/element-data-loader"
-
Install
element-data-loader
withCaImAn
requires two separate commandspip install "element-data-loader[caiman_requirements] @ git+https://github.com/datajoint/element-data-loader" pip install "element-data-loader[caiman] @ git+https://github.com/datajoint/element-data-loader"
-
Install
element-data-loader
with multiple packagespip install "element-data-loader[caiman_requirements] @ git+https://github.com/datajoint/element-data-loader" pip install "element-data-loader[scanreader,sbxreader,suite2p,caiman] @ git+https://github.com/datajoint/element-data-loader"
-
- See workflow-calcium-imaging
repository for an example usage of
element-calcium-imaging
.