Phenotypic variation of transcriptomic cell types in mouse motor cortex (paper). Scientist got neurons from different layers and regions and compared their DNA. That added to the classification by neuron's form because generation of enzymes and transmitters is coded in DNA, thus we probably can tell more about neuron's functions now.
Get data
- install SQLAlchemy, neuroanalysis
pip install SQLAlchemy neuroanalysis - download API
git clone https://github.com/AllenInstitute/aisynphys.git cd aisynphys &&- install
python setup.py install - start Python (I use 3.8.1)
python - import
from aisynphys.database import SynphysDatabase - get a list of versions (sort by size)
l = SynphysDatabase.list_versions()
l.sort(reverse=True, key=lambda x: x['db_size'])
for f in l:
print(f['db_file'], f['db_size'])Output:
synphys_r1.0_2019-08-29_small.sqlite small
synphys_r1.0_small.sqlite small
synphys_r2.0-pre1_small.sqlite small
synphys_r2.0-pre2_small.sqlite small
synphys_r2.0-pre3_small.sqlite small
synphys_r2.0-pre4_small.sqlite small
synphys_r2.0-pre5_small.sqlite small
synphys_r2.0_small.sqlite small
synphys_r1.0_2019-08-29_medium.sqlite medium
synphys_r1.0_medium.sqlite medium
synphys_r2.0-pre1_medium.sqlite medium
synphys_r2.0-pre2_medium.sqlite medium
synphys_r2.0-pre3_medium.sqlite medium
synphys_r2.0-pre4_medium.sqlite medium
synphys_r2.0-pre5_medium.sqlite medium
synphys_r2.0_medium.sqlite medium
synphys_r1.0_2019-08-29_full.sqlite full
synphys_r1.0_full.sqlite full
synphys_r2.0-pre1_full.sqlite full
synphys_r2.0_full.sqlite full- download
import aisynphys
aisynphys.config.cache_path = r"C:\Users\neupo\ai\brain_map"
db = SynphysDatabase.load_version('synphys_r2.0_small.sqlite')Display it?
https://portal.brain-map.org/explore/toolkit/morpho-reconstruction/vaa3d-mozak