Metadata-Version: 2.1
Name: ndx-multichannel-volume
Version: 0.1.3
Summary: extension to allow use of multichannel volumetric images
Home-page: 
Author: Daniel Sprague
Author-email: daniel.sprague@ucsf.edu
License: BSD-3
Keywords: NeurodataWithoutBorders,NWB,nwb-extension,ndx-extension
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Description-Content-Type: text/markdown; charset=UTF-8
License-File: LICENSE.txt
Requires-Dist: pynwb (<3,>=1.5.0)
Requires-Dist: hdmf (<4,>=2.5.6)

# ndx-multichannel-volume Extension for NWB

This extension is to add support for volumetric multichannel images. This
extends existing NWB functions for optophysiology imaging to allow for 
3 dimensions and a flexible number of channels. There is additional support
for adding metadata that is necessary for imaging in C. Elegans.

## Installation

To install this package on Unix/macOS, run in command line
python3 -m pip install --index-url https://pypi.org/simple/ --no-deps ndx-multichannel-volume

On windows, run 

py -m pip install --index-url https://pypi.org/simple/ --no-deps ndx-multichannel-volume


## Usage

This extension is to add support for volumetric multichannel images. This 
extends existing NWB functions for optophysiology imaging to allow for 
3 dimensions and a flexible number of channels. There is additional support
for adding metadata that is necessary for imaging in C. Elegans. 

New classes added in this extension are:

CElegansSubject - extension of the base subject class with additional attributes
for metadata specific to C. Elegans.

MultiChannelVolumeSeries - extension of the base TimeSeries class to support 
multiple channels and 3 dimensions.

MultiChannelVolume - class for storing mutlichannel volumetric images with 
a flexible number of channels. 

ImagingVolume - alternate version of the native ImagingPlane class for supporting
metadata associated with volumetric multichannel images. Contains a list of optical
channel references as well as an ordered list of how those channels index to the 
channels in the image.

OpticalChannelPlus - extension of the OpticalChannel class to support additional
information including emission_range, excitation_range, and excitation_lambda.

OpticalChannelReferences - contains ordered list of optical channel to represent the 
order of the optical channels in the reference volume.

VolumeSegmentation - contains segmentation masks for image volumes. There are options 
to use either a standard voxel_mask with XYZ information as well as a Cell ID label,
or color_voxel_mask which has RGBW information as well as XYZ.

Please see https://github.com/focolab/ndx-multichannel-volume/blob/main/src/pynwb/create_NWB.ipynb for example code on how to use these new data types/classes

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This extension was created using [ndx-template](https://github.com/nwb-extensions/ndx-template).
