mirror of
https://github.com/p2p-ld/nwb-linkml.git
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360 lines
12 KiB
YAML
360 lines
12 KiB
YAML
groups:
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- neurodata_type_def: OnePhotonSeries
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neurodata_type_inc: ImageSeries
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doc: Image stack recorded over time from 1-photon microscope.
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attributes:
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- name: pmt_gain
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dtype: float32
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doc: Photomultiplier gain.
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required: false
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- name: scan_line_rate
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dtype: float32
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doc: Lines imaged per second. This is also stored in /general/optophysiology but
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is kept here as it is useful information for analysis, and so good to be stored
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w/ the actual data.
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required: false
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- name: exposure_time
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dtype: float32
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doc: Exposure time of the sample; often the inverse of the frequency.
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required: false
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- name: binning
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dtype: uint8
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doc: Amount of pixels combined into 'bins'; could be 1, 2, 4, 8, etc.
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required: false
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- name: power
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dtype: float32
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doc: Power of the excitation in mW, if known.
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required: false
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- name: intensity
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dtype: float32
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doc: Intensity of the excitation in mW/mm^2, if known.
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required: false
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links:
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- name: imaging_plane
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target_type: ImagingPlane
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doc: Link to ImagingPlane object from which this TimeSeries data was generated.
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- neurodata_type_def: TwoPhotonSeries
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neurodata_type_inc: ImageSeries
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doc: Image stack recorded over time from 2-photon microscope.
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attributes:
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- name: pmt_gain
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dtype: float32
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doc: Photomultiplier gain.
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required: false
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- name: scan_line_rate
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dtype: float32
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doc: Lines imaged per second. This is also stored in /general/optophysiology but
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is kept here as it is useful information for analysis, and so good to be stored
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w/ the actual data.
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required: false
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datasets:
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- name: field_of_view
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dtype: float32
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dims:
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- - width|height
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- - width|height|depth
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shape:
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- - 2
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- - 3
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doc: Width, height and depth of image, or imaged area, in meters.
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quantity: '?'
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links:
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- name: imaging_plane
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target_type: ImagingPlane
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doc: Link to ImagingPlane object from which this TimeSeries data was generated.
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- neurodata_type_def: RoiResponseSeries
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neurodata_type_inc: TimeSeries
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doc: ROI responses over an imaging plane. The first dimension represents time.
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The second dimension, if present, represents ROIs.
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datasets:
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- name: data
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dtype: numeric
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dims:
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- - num_times
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- - num_times
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- num_ROIs
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shape:
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- - null
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- - null
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- null
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doc: Signals from ROIs.
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- name: rois
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neurodata_type_inc: DynamicTableRegion
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doc: DynamicTableRegion referencing into an ROITable containing information on the ROIs
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stored in this timeseries.
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- neurodata_type_def: DfOverF
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neurodata_type_inc: NWBDataInterface
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default_name: DfOverF
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doc: dF/F information about a region of interest (ROI). Storage hierarchy of dF/F
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should be the same as for segmentation (i.e., same names for ROIs and for image
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planes).
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groups:
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- neurodata_type_inc: RoiResponseSeries
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doc: RoiResponseSeries object(s) containing dF/F for a ROI.
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quantity: '+'
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- neurodata_type_def: Fluorescence
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neurodata_type_inc: NWBDataInterface
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default_name: Fluorescence
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doc: Fluorescence information about a region of interest (ROI). Storage hierarchy
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of fluorescence should be the same as for segmentation (ie, same names for ROIs
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and for image planes).
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groups:
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- neurodata_type_inc: RoiResponseSeries
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doc: RoiResponseSeries object(s) containing fluorescence data for a ROI.
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quantity: '+'
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- neurodata_type_def: ImageSegmentation
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neurodata_type_inc: NWBDataInterface
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default_name: ImageSegmentation
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doc: Stores pixels in an image that represent different regions of interest (ROIs)
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or masks. All segmentation for a given imaging plane is stored together, with
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storage for multiple imaging planes (masks) supported. Each ROI is stored in its
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own subgroup, with the ROI group containing both a 2D mask and a list of pixels
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that make up this mask. Segments can also be used for masking neuropil. If segmentation
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is allowed to change with time, a new imaging plane (or module) is required and
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ROI names should remain consistent between them.
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groups:
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- neurodata_type_inc: PlaneSegmentation
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doc: Results from image segmentation of a specific imaging plane.
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quantity: '+'
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- neurodata_type_def: PlaneSegmentation
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neurodata_type_inc: DynamicTable
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doc: Results from image segmentation of a specific imaging plane.
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datasets:
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- name: image_mask
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neurodata_type_inc: VectorData
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dims:
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- - num_roi
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- num_x
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- num_y
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- - num_roi
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- num_x
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- num_y
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- num_z
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shape:
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- - null
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- null
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- null
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- - null
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- null
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- null
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- null
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doc: ROI masks for each ROI. Each image mask is the size of the original imaging
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plane (or volume) and members of the ROI are finite non-zero.
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quantity: '?'
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- name: pixel_mask_index
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neurodata_type_inc: VectorIndex
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doc: Index into pixel_mask.
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quantity: '?'
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- name: pixel_mask
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neurodata_type_inc: VectorData
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dtype:
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- name: x
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dtype: uint32
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doc: Pixel x-coordinate.
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- name: y
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dtype: uint32
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doc: Pixel y-coordinate.
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- name: weight
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dtype: float32
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doc: Weight of the pixel.
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doc: 'Pixel masks for each ROI: a list of indices and weights for the ROI. Pixel
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masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation'
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quantity: '?'
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- name: voxel_mask_index
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neurodata_type_inc: VectorIndex
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doc: Index into voxel_mask.
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quantity: '?'
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- name: voxel_mask
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neurodata_type_inc: VectorData
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dtype:
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- name: x
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dtype: uint32
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doc: Voxel x-coordinate.
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- name: y
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dtype: uint32
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doc: Voxel y-coordinate.
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- name: z
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dtype: uint32
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doc: Voxel z-coordinate.
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- name: weight
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dtype: float32
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doc: Weight of the voxel.
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doc: 'Voxel masks for each ROI: a list of indices and weights for the ROI. Voxel
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masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation'
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quantity: '?'
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groups:
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- name: reference_images
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doc: Image stacks that the segmentation masks apply to.
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groups:
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- neurodata_type_inc: ImageSeries
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doc: One or more image stacks that the masks apply to (can be one-element
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stack).
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quantity: '*'
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links:
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- name: imaging_plane
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target_type: ImagingPlane
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doc: Link to ImagingPlane object from which this data was generated.
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- neurodata_type_def: ImagingPlane
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neurodata_type_inc: NWBContainer
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doc: An imaging plane and its metadata.
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datasets:
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- name: description
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dtype: text
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doc: Description of the imaging plane.
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quantity: '?'
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- name: excitation_lambda
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dtype: float32
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doc: Excitation wavelength, in nm.
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- name: imaging_rate
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dtype: float32
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doc: Rate that images are acquired, in Hz. If the corresponding TimeSeries is present, the rate should be stored
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there instead.
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quantity: '?'
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- name: indicator
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dtype: text
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doc: Calcium indicator.
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- name: location
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dtype: text
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doc: Location of the imaging plane. Specify the area, layer, comments on estimation
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of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas
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names for anatomical regions when possible.
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- name: manifold
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dtype: float32
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dims:
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- - height
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- width
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- x, y, z
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- - height
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- width
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- depth
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- x, y, z
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shape:
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- - null
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- null
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- 3
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- - null
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- null
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- null
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- 3
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doc: "DEPRECATED Physical position of each pixel. 'xyz' represents the position\
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\ of the pixel relative to the defined coordinate space. Deprecated in favor of origin_coords and grid_spacing."
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quantity: '?'
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attributes:
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- name: conversion
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dtype: float32
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default_value: 1.0
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doc: Scalar to multiply each element in data to convert it to the specified 'unit'.
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If the data are stored in acquisition system units or other units
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that require a conversion to be interpretable, multiply the data by 'conversion'
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to convert the data to the specified 'unit'. e.g. if the data acquisition system
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stores values in this object as pixels from x = -500 to 499, y = -500 to 499
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that correspond to a 2 m x 2 m range, then the 'conversion' multiplier to get
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from raw data acquisition pixel units to meters is 2/1000.
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required: false
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- name: unit
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dtype: text
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default_value: meters
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doc: Base unit of measurement for working with the data. The default value is 'meters'.
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required: false
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- name: origin_coords
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dtype: float32
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dims:
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- - x, y
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- - x, y, z
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shape:
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- - 2
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- - 3
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doc: Physical location of the first element of the imaging plane (0, 0) for 2-D data or (0, 0, 0) for 3-D data.
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See also reference_frame for what the physical location is relative to (e.g., bregma).
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quantity: '?'
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attributes:
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- name: unit
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dtype: text
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default_value: meters
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doc: Measurement units for origin_coords. The default value is 'meters'.
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- name: grid_spacing
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dtype: float32
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dims:
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- - x, y
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- - x, y, z
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shape:
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- - 2
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- - 3
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doc: Space between pixels in (x, y) or voxels in (x, y, z) directions, in the specified unit.
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Assumes imaging plane is a regular grid. See also reference_frame to interpret the grid.
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quantity: '?'
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attributes:
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- name: unit
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dtype: text
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default_value: meters
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doc: Measurement units for grid_spacing. The default value is 'meters'.
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- name: reference_frame
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dtype: text
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doc: Describes reference frame of origin_coords and grid_spacing.
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For example, this can be a text description of the anatomical location and orientation of the grid
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defined by origin_coords and grid_spacing or the vectors needed to transform or rotate the grid to
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a common anatomical axis (e.g., AP/DV/ML). This field is necessary to interpret origin_coords and grid_spacing.
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If origin_coords and grid_spacing are not present, then this field is not required.
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For example, if the microscope takes 10 x 10 x 2 images, where the first value of the data matrix
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(index (0, 0, 0)) corresponds to (-1.2, -0.6, -2) mm relative to bregma, the spacing between pixels is 0.2 mm in
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x, 0.2 mm in y and 0.5 mm in z, and larger numbers in x means more anterior, larger numbers in y means more
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rightward, and larger numbers in z means more ventral, then enter the following --
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origin_coords = (-1.2, -0.6, -2)
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grid_spacing = (0.2, 0.2, 0.5)
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reference_frame = "Origin coordinates are relative to bregma. First dimension corresponds to anterior-posterior
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axis (larger index = more anterior). Second dimension corresponds to medial-lateral axis (larger index = more
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rightward). Third dimension corresponds to dorsal-ventral axis (larger index = more ventral)."
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quantity: '?'
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groups:
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- neurodata_type_inc: OpticalChannel
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doc: An optical channel used to record from an imaging plane.
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quantity: '+'
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links:
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- name: device
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target_type: Device
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doc: Link to the Device object that was used to record from this electrode.
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- neurodata_type_def: OpticalChannel
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neurodata_type_inc: NWBContainer
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doc: An optical channel used to record from an imaging plane.
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datasets:
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- name: description
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dtype: text
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doc: Description or other notes about the channel.
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- name: emission_lambda
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dtype: float32
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doc: Emission wavelength for channel, in nm.
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- neurodata_type_def: MotionCorrection
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neurodata_type_inc: NWBDataInterface
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default_name: MotionCorrection
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doc: 'An image stack where all frames are shifted (registered) to a common coordinate
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system, to account for movement and drift between frames. Note: each frame at
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each point in time is assumed to be 2-D (has only x & y dimensions).'
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groups:
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- neurodata_type_inc: CorrectedImageStack
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doc: Reuslts from motion correction of an image stack.
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quantity: '+'
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- neurodata_type_def: CorrectedImageStack
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neurodata_type_inc: NWBDataInterface
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doc: Reuslts from motion correction of an image stack.
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groups:
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- name: corrected
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neurodata_type_inc: ImageSeries
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doc: Image stack with frames shifted to the common coordinates.
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- name: xy_translation
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neurodata_type_inc: TimeSeries
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doc: Stores the x,y delta necessary to align each frame to the common coordinates,
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for example, to align each frame to a reference image.
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links:
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- name: original
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target_type: ImageSeries
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doc: Link to ImageSeries object that is being registered.
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