createImageFromTiffs

createImageFromTiffs.py

# See https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=8679
# and https://www.openmicroscopy.org/community/posting.php?mode=reply&f=6&t=8706

import omero
from omero.gateway import BlitzGateway
from PIL import Image
import numpy

conn = BlitzGateway("username", "password", host="localhost", port=4064)
conn.connect()

dataset = conn.getObject("Dataset", 25604)

# ----------- READ multiple TIFFs ---------------------------
image_paths = ["/path/to/image1.tif",
    "/path/to/image2.tif"]

sizeC = len(image_paths)
imageName = "imageFromTiffs"

def plane_generator():
    for path_to_image in image_paths:
        img = Image.open(path_to_image)
        # If this is an rgb tiff you may need to split the channels
        np_array = numpy.asarray(img)
        yield np_array

plane_gen = plane_generator()
newImg = conn.createImageFromNumpySeq(
        plane_gen, imageName, sizeZ=1, sizeC=sizeC, sizeT=1, description='Test', dataset=dataset)

print "Created new Image:", newImg.id