napari_cosem.py

import zarr
import napari
import click

# Challenge napari with some big data. 
# Compare with how neuroglancer handles the same dataset: 
# http://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22:%7B%22x%22:%5B4e-9%2C%22m%22%5D%2C%22y%22:%5B4e-9%2C%22m%22%5D%2C%22z%22:%5B4e-9%2C%22m%22%5D%7D%2C%22position%22:%5B5877.4033203125%2C7050.5%2C5252.34033203125%5D%2C%22crossSectionScale%22:36.598234443678%2C%22projectionScale%22:16384%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22n5://https://janelia-cosem-datasets.s3.amazonaws.com/jrc_fly-fsb-1/jrc_fly-fsb-1.n5/em/fibsem-uint16%22%2C%22tab%22:%22rendering%22%2C%22shaderControls%22:%7B%22normalized%22:%7B%22range%22:%5B1773%2C4458%5D%7D%7D%2C%22name%22:%22fibsem-uint16%22%7D%5D%2C%22selectedLayer%22:%7B%22visible%22:true%2C%22layer%22:%22fibsem-uint16%22%7D%2C%22layout%22:%224panel%22%7D

containerPath = 's3://janelia-cosem-datasets/jrc_fly-fsb-1/jrc_fly-fsb-1.n5'
groupPath = 'em/fibsem-uint16'

@click.command()
@click.argument('mode', type=str, default='easy')
def show_n5(containerPath=containerPath, groupPath=groupPath, mode='easy'):
    contrast_limits=(0,4700)
    cmap = 'gray_r' 
    group = zarr.open(zarr.N5FSStore(containerPath), path=groupPath)
    # get multiscale pyramid as a list of arrays
    arrays = list(dict(group.arrays()).values())
    click.echo(arrays)
    if mode == 'easy':      
        # show the smallest array
        to_show = arrays[-1]
    elif mode == 'hard':
        # show the full pyramid
        to_show = arrays
    else: 
        raise ValueError("Mode {mode} not recognized. Choose from `easy` or `hard`")
    
    viewer = napari.view_image(to_show, contrast_limits=contrast_limits, colormap=cmap)
    napari.run()

if __name__ == '__main__': 
    show_n5()