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Add new catalog entry for ndx-multichannel-volume (#38)
Co-authored-by: dysprague <[email protected]> Co-authored-by: Ryan Ly <[email protected]>
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# ndx-multichannel-volume Extension for NWB | ||
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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. | ||
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## Installation | ||
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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 | ||
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On windows, run | ||
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py -m pip install --index-url https://pypi.org/simple/ --no-deps ndx-multichannel-volume | ||
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## Usage | ||
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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. | ||
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New classes added in this extension are: | ||
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CElegansSubject - extension of the base subject class with additional attributes | ||
for metadata specific to C. Elegans. | ||
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MultiChannelVolumeSeries - extension of the base TimeSeries class to support | ||
multiple channels and 3 dimensions. | ||
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MultiChannelVolume - class for storing mutlichannel volumetric images with | ||
a flexible number of channels. | ||
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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. | ||
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OpticalChannelPlus - extension of the OpticalChannel class to support additional | ||
information including emission_range, excitation_range, and excitation_lambda. | ||
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OpticalChannelReferences - contains ordered list of optical channel to represent the | ||
order of the optical channels in the reference volume. | ||
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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. | ||
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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). |
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name: ndx-multichannel-volume | ||
version: 0.1.12 | ||
src: https://github.com/focolab/ndx-multichannel-volume | ||
pip: https://pypi.org/project/ndx-multichannel-volume/ | ||
license: BSD-3 | ||
maintainers: | ||
- dysprague | ||
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