A count of the total number of mitochondria within the bounds (694×1794, 1750×2460, 1004×1379).



In [1]:

    
import ndio.remote.OCP as OCP
oo = OCP()



In [4]:

    
token = "kasthuri2015_ramon_v1"

We can count annotated mitochondria by referencing the mitochondria channel:



In [15]:

    
mito_cutout = oo.get_cutout(token, 'mitochondria', 694, 1794, 1750, 2460, 1004, 1379, resolution=3)

We can now use the built-in connected-components to count mitochondria.



In [16]:

    
import ndio.utils.stats as ndstats



In [17]:

    
c, f = ndstats.connected_components(mito_cutout)



In [18]:

    
print "There are {} mitochondria total in the annotated volume.".format(f)









    



There are 1967 mitochondria total in the annotated volume.