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