Collections / Eye-conic' spatial transcriptomics of keratoconus corneas

Eye-conic' spatial transcriptomics of keratoconus corneas

The cornea is a transparent, avascular eye tissue composed of five layers: epithelium, Bowman's layer, stroma, Descemet's membrane, and endothelium, each of which, if affected by keratoconus (KTCN), may exhibit specific morphological changes. Due to the complexity of the tissue, the studies preserving the spatial location should be applied to identify the layer-specific molecular changes in KTCN, for further understanding of the mechanistic aspects of its cone formation. Study was supported by National Science Centre in Poland, Grant no. 2021/41/B/NZ5/02245 (MG).

Datasets13
Size~136 MB
AssayVisium
Samplehuman · cornea
KindComparison
Flag a data issue
PMID:41931003 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse303036")
cohort.members        # the 13 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/")
Install (Python 3.12+) Docs →
Python · lamindb

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-gse303036")
coll.ordered_artifacts.to_dataframe()   # the 13 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]
Install (Python 3.12+) Docs →
Shell 
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse303036 --dest data/
Install (Python 3.12+) Docs →

Licenses: 13 NCBI GEO policy

Member datasets · 13
Open in Vitessce
Visium
Human cornea
GSM9116180
human cornea 9.5 MB 1,556 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuecornea
Size9.5 MB
Spots1,556
Magnificationother · 3.868 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Visium
Human cornea
GSM9116170
human cornea keratoconus 11.4 MB 1,036 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuecornea
Conditionkeratoconus
Size11.4 MB
Spots1,036
Magnificationother · 3.813 µm/px
bronze H&E NCBI GEO policy
Open in Vitessce
Visium
Human cornea
GSM9116172
human cornea keratoconus 11.4 MB 1,065 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuecornea
Conditionkeratoconus
Size11.4 MB
Spots1,065
Magnificationother · 3.868 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human cornea
GSM9116174
human cornea keratoconus 12.2 MB 1,291 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuecornea
Conditionkeratoconus
Size12.2 MB
Spots1,291
Magnificationother · 3.868 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human cornea
GSM9116175
human cornea keratoconus 10.1 MB 1,646 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuecornea
Conditionkeratoconus
Size10.1 MB
Spots1,646
Magnificationother · 3.866 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human cornea
GSM9116176
human cornea 9.3 MB 1,505 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuecornea
Size9.3 MB
Spots1,505
Magnificationother · 3.868 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human cornea
GSM9116171
human cornea keratoconus 10.9 MB 1,575 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuecornea
Conditionkeratoconus
Size10.9 MB
Spots1,575
Magnificationother · 3.866 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human cornea
GSM9116178
human cornea 10.1 MB 1,727 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuecornea
Size10.1 MB
Spots1,727
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human cornea
GSM9116173
human cornea keratoconus 10.3 MB 1,226 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuecornea
Conditionkeratoconus
Size10.3 MB
Spots1,226
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human cornea
GSM9116177
human cornea 11.2 MB 2,357 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuecornea
Size11.2 MB
Spots2,357
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human cornea
GSM9116169
human cornea keratoconus 9.9 MB 950 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuecornea
Conditionkeratoconus
Size9.9 MB
Spots950
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human cornea
GSM9116181
human cornea keratoconus 9.4 MB 1,368 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuecornea
Conditionkeratoconus
Size9.4 MB
Spots1,368
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human cornea
GSM9116179
human cornea 10.6 MB 1,886 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuecornea
Size10.6 MB
Spots1,886
Magnificationother · 3.866 µm/px
bronze H&E NCBI GEO policy Open in Vitessce

Cite this collection

doi.org/10.1167/iovs.67.4.7 ↗
BibTeX 
@article{Wysocka_2026,
  title = {“Eye-Conic” Spatial Transcriptomics Reveals the Layer-Specific Molecular Alterations in Corneas of Patients With Keratoconus},
  volume = {67},
  ISSN = {1552-5783},
  url = {http://dx.doi.org/10.1167/iovs.67.4.7},
  DOI = {10.1167/iovs.67.4.7},
  number = {4},
  journal = {Investigative Ophthalmology & Visual Science},
  publisher = {Association for Research in Vision and Ophthalmology (ARVO)},
  author = {Wysocka, Alicja and Jaskiewicz-Rajewicz, Katarzyna and Wozniak, Jakub and Rydzanicz, Malgorzata and Ploski, Rafal and Udziela, Monika and Szaflik, Jacek P. and Gajecka, Marzena},
  year = {2026},
  month = Apr,
  pages = {7}
}