ndx-multichannel-volume 0.1.12

extension to allow use of multichannel volumetric images

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.