saving dF/F traces with pynwb

ophys_example.py

# NOTE: `dataset` is an internal object for data ingest & time alignment

session_start_time = dataset.pkl['startdatetime']
roi_masks = dataset.get_roi_mask_array()
max_projection = dataset.get_max_projection()

dFF, dFF_t = dataset.get_dff_traces()

NA = 'THIS REQUIRED ATTRIBUTE INTENTIONALLY LEFT BLANK.'


from pynwb import NWBFile
nwb = NWBFile(
    source = NA, 
    session_description = NA, 
    identifier = NA, 
    session_start_time = session_start_time,
)

from pynwb import ophys
optical_channel = ophys.OpticalChannel(
    name = 'Optical Channel',
    source = NA,
    description = NA,
    emission_lambda = NA,
)

from pynwb import image
max_proj = image.ImageSeries(
    name = 'Maximum Projection Image',
    source = NA,
    data = max_projection,
    unit = NA,
    format = 'raw',
    timestamps = [0.0], # <- This is required, so let's make it at the beginning of the experiment
)

roi_list = []
for ii, mask in enumerate(roi_masks):
    roi_list.append(
        ophys.ROI(
            name = str(ii),
            source = NA,
            roi_description = NA,
            pix_mask = [],
            pix_mask_weight = [],
            img_mask = mask,
            reference_images = max_proj, # <- Ugh, I need to define reference image(s) just to define an ROI?
        )
    )

imaging_plane = ophys.ImagingPlane(
    name = 'Imaging Plane',
    source = NA,
    optical_channel = optical_channel, # <- Ugh, I need to define an OpticalChannel just to define an ImagingPlane?
    description = NA, # <- Why is this required?
    device = 'scientifica', # <- this is an implicit link to /general/devices [device (str): Name of device in /general/devices]
    excitation_lambda = "910nm", # <- this should be a float or int with a "units" field
    imaging_rate = NA, # <- why is this required? & why is it a string?
    indicator = NA,
    location = NA,
    manifold = [], # <- I don't understand what this is.
    conversion = 1.0,
    unit = 'um',
    reference_frame = NA,
)

segmentation = ophys.PlaneSegmentation(
    name = 'Plane Segmentation',
    source = NA,
    description = NA,
    roi_list = roi_list, # <- Ugh, I need to define a list of ROIs just to define an PlaneSegmentation?
    imaging_plane = imaging_plane, # <- Ugh, I need to define an imaging plane just to define a PlaneSegmentation?
    reference_images = max_proj,
)

seg_interface = ophys.ImageSegmentation(
    name = 'Image Segmentation', 
    source = NA, 
    plane_segmentation = segmentation, # <- Ugh, I need to define an segmentation just to store calcium traces?
)

dFF_series = ophys.RoiResponseSeries(
    name = 'dF/F',
    source = NA,
    data = dFF,
    unit = 'dF/F',
    roi_names = [roi.name for roi in roi_list], # <- shouldn't this be a more explicit link to the ROIs?
    segmenttation_interface = seg_interface, # <- Ugh, I need to define an interface just to store calcium traces?
    timestamps = dFF_t,
)

dFF = ophys.DfOverF(
    source = NA,
    roi_response_series = dFF_series, # <- Wait, this object is just a wrapper for an RoiResponseSeries? 
)

# not let's create the processing module to store this in
ophys_module = nwb.create_processing_module(
    name="ophys",
    description="calcium responses",
    source="Allen Brain Observatory: Visual Behavior",
)

# what happens if we only add one container?
ophys_module.add_container(dFF)