I was downloading some connectivity data through the AllenSKD package. I want to have connection data from all the brain structures, projecting to a specific target, so i did:
# import libraries and API
from allensdk.core.mouse_connectivity_cache import MouseConnectivityCache
from pathlib import Path
output_dir = './data'
# fetch the data
mcc = MouseConnectivityCache(manifest_file=Path(output_dir) / 'manifest.json')
# hierarchical list of mouse brain structures
structure_tree = mcc.get_structure_tree()
# Get the target structure of interest (SLC)
slc = structure_tree.get_structures_by_acronym(['SLC'])[0]
# Retrieve all experiments (wild-type)
all_exp = mcc.get_experiments(cre=False, injection_structure_ids=None)
# Retrieve unionized data for projections to SLC
proj_to_slc = mcc.get_structure_unionizes(
[e['id'] for e in all_exp], # projection sources structures (all experiments)
is_injection=False, # Data for non-injection sites
structure_ids=[slc['id']], # Target SLC structure
include_descendants=True
)
(please tell me also if its the correct approach, since I’ve modified it a bit from the examples provided from the website).
So, I’ve noticed that the data (of projection_density) retrieved in this way are different from the value of the same experiments that is possible to download manually directly from the Mouse Connectivity Projection webpage (webpage).
Can anyone help me in understanding why? is there any modification done?
to have a more detailed explanation of the situation i’ve also wrote another post here
Thank you to everyone who can help me solve those issues!