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