Skip to content

Commit

Permalink
Add new catalog entry for ndx-multichannel-volume (#38)
Browse files Browse the repository at this point in the history
Co-authored-by: dysprague <[email protected]>
Co-authored-by: Ryan Ly <[email protected]>
  • Loading branch information
3 people authored Mar 31, 2024
1 parent f1ed4df commit bd382b5
Show file tree
Hide file tree
Showing 2 changed files with 62 additions and 0 deletions.
54 changes: 54 additions & 0 deletions ndx-multichannel-volume/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,54 @@
# 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).
8 changes: 8 additions & 0 deletions ndx-multichannel-volume/ndx-meta.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
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

0 comments on commit bd382b5

Please sign in to comment.