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: Results from motion correction of an image stack. quantity: '+' - neurodata_type_def: CorrectedImageStack neurodata_type_inc: NWBDataInterface doc: Results 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.