reproduce https://github.com/NeurodataWithoutBorders/pynwb/issues/550

pix_mask.py

from datetime import datetime
from pynwb import NWBFile, NWBHDF5IO
from pynwb.ophys import ImageSegmentation, TwoPhotonSeries, OpticalChannel

nwbfile = NWBFile('a', 'b', 'c', datetime.now())

mod = nwbfile.create_processing_module('a', 'b', 'c')

optical_channel = OpticalChannel('a', 'b', 'c', 500.)

imaging_plane = nwbfile.create_imaging_plane('a', 'b', optical_channel, 'c', 'd', 600., '2.718', 'GFP', 'd', [], 4.0, 'e', 'f')

image_series = TwoPhotonSeries(
    name='a',
    source='b',
    dimension=[2],
    external_file=['images.tiff'],
    imaging_plane=imaging_plane,
    starting_frame=[0],
    format='tiff',
    timestamps=list())

nwbfile.add_acquisition(image_series)

mod = nwbfile.create_processing_module('my_ca_imaging_module', 'b', 'c')
img_seg = ImageSegmentation('desc')
mod.add_data_interface(img_seg)
ps = img_seg.create_plane_segmentation('b', 'c', imaging_plane, 'my_planeseg', image_series)

# 3d pix_mask format: [(x, y, z, val)]
pix_mask1 = [(1, 2, 3, 1.1)]
img_mask1 = [[1.1, 0.0, 0.0]]
ps.add_roi('1234', pix_mask1, img_mask1)

io = NWBHDF5IO('example.nwb', 'w')
io.write(nwbfile)