Calcium Imaging DataJoint element
Project 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 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 forScanLocation
-
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 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)
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 particularScanInfo.Field
-
MaskClassification
- classification ofSegmentation.Mask
into different type (e.g. soma, axon, dendrite, artifact, etc.)
Neural activity extraction
-
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)
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, to install:
pip install git+https://github.com/atlab/scanreader.git
Element usage
- See workflow-calcium-imaging
repository for an example usage of
element-calcium-imaging
.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for element-calcium-imaging-0.1.0b0.tar.gz
Algorithm | Hash digest | |
---|---|---|
SHA256 | 82e00e7bc8ce7a1dd10f80ce65aad9e3e0012d39dc223624963c5beec8e65609 |
|
MD5 | 1a8cfdb5ed51b2d4cea94ea901482aa9 |
|
BLAKE2b-256 | a0e93d7ec46541a752f9f1b4937f5c29659dc25b9db7ee37d05e3cb3784d1284 |
Hashes for element_calcium_imaging-0.1.0b0-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 416226606a46613fdd76f1e7c8b0d7138591660fbd0b209e0759e67da0b1d641 |
|
MD5 | 18d7a537f607427d9d36e6f3d263e374 |
|
BLAKE2b-256 | 6bcbf331b370dc989b41b5052243c6820e0da24a5e4aa1af1f9af07af820d68c |