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



In [1]:

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



In [2]:

    
token = "kasthuri2015_ramon_v1"

We can count annotated vesicles by referencing the vesicle channel:



In [8]:

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

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



In [5]:

    
import ndio.utils.stats as ndstats



In [6]:

    
c, f = ndstats.connected_components(mito_cutout)



In [9]:

    
print "There are {} vesicles total in the annotated volume. (Is this channel unpopulated‽)".format(f)









    



There are 0 vesicles total in the annotated volume. (Is this channel unpopulated‽)