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