Focal cortical dysplasia (FCD) is a severe neurodevelopmental malformation that often manifests as medically refractory epilepsy. A key histological hallmark of FCD is the presence of cytomegalic dysmorphic neurons (CDNs), which are considered to be major contributors to cortical network hyperexcitability. However, the relatively low frequency of CDNs within resected lesions has challenged their unbiased molecular characterization. Here, we leverage deep learning approaches to objectively map key anatomical compartments of FCD and guide regional spatial transcriptomic profiling. Using this approach, we generate an anatomical transcriptional catalog of type IIb FCD, and uncover non-canonical markers of signaling and neurotransmitter pathways in CDNs that may serve as new therapeutic targets for this debilitating disorder.
from sddb import Catalog
cohort = Catalog().collection("geo-gse300645")
cohort.members # the 4 datasets as a table
print(cohort.licenses()) # check the terms before you download
sdatas = cohort.to_dict() # {uid: SpatialData}, cached locally
# or keep the .zarr files in a folder of your choice:
# sdatas = cohort.to_dict(dest="data/")Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
coll = db.Collection.get(key="geo-gse300645")
coll.ordered_artifacts.to_dataframe() # the 4 members, ordered
# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse300645 --dest data/Licenses: 4 NCBI GEO policy
@article{Paliwal_2025,
title = {Dysmorphic neurons express markers of inhibitory glycinergic signaling in focal cortical dysplasia
<scp>IIb</scp>},
volume = {36},
ISSN = {1750-3639},
url = {http://dx.doi.org/10.1111/bpa.70043},
DOI = {10.1111/bpa.70043},
number = {2},
journal = {Brain Pathology},
publisher = {Wiley},
author = {Paliwal, Ameesha and Faust, Kevin and Borhani, Okty Abbasi and Liu, Mugeng and Omoto, Lauren and Kamski‐Hennekam, Evelyn Rose and Zadeh, Parsa Babaei and Sajid, Rifat Shahriar and Diamandis, Phedias},
year = {2025},
month = Sept
}