pythonstacktiff

Save TIFF stack with different metadata

I have multiple photos from microscope in the form of numpy arrays and I want to store them in a single multistack TIFF file. They represent the same XY point but in different heights. I want that each slide has its own metadata where it stores information specific to that photo. This is what I have been trying using the tifffile library):

metadata = {'x': 10.5, 'y': 7.5}
with tifffile.TiffWriter(filename, bigtiff=False, imagej=False) as tif_writer:
     for z_slice in xyz_stack:
         metadata["z"] = z_slice.z
         tif_writer.write(z_slice.numpy_array, description=json.dumps(metadata))

But this doesn't work, as it puts the same description to all slices. How can I achieve this?

Thanks! :)

Solution

  • For images from microscopy, consider writing OME-TIFF files. This example writes a Z stack with metadata specifying the position of each plane:

    import numpy
from tifffile import TiffWriter

data = numpy.random.randint(0, 1023, (8, 256, 256), 'uint16')
pixelsize = 0.29  # micrometer
zpositions = [0.0, 1.1, 2.2, 3.3, 4.4, 5.5, 6.6, 7.7]
metadata = {
    'axes': 'ZYX',
    'SignificantBits': 10,
    'PhysicalSizeX': pixelsize,
    'PhysicalSizeXUnit': 'µm',
    'PhysicalSizeY': pixelsize,
    'PhysicalSizeYUnit': 'µm',
    'Plane': {
        'PositionZ': zpositions,
        'PositionZUnit': ['µm'] * data.shape[0],
        'PositionY': [7.5] * data.shape[1],
        'PositionYUnit': ['µm'] * data.shape[1],
        'PositionX': [10.5] * data.shape[2],
        'PositionXUnit': ['µm'] * data.shape[2],
    },
}

with TiffWriter('temp.ome.tif', bigtiff=False, ome=True) as tif:
    tif.write(
        data,
        photometric='minisblack',
        # tile=(128, 128),
        # compression='adobe_deflate',
        resolutionunit='CENTIMETER',
        resolution=(1e4 / pixelsize, 1e4 / pixelsize),
        metadata=metadata,
    )