Volumetric Cyclic Immunofluorescence for 3D Spatial Profiling of Immune Structures in Human FFPE Tissue
- GENERAL INFORMATION
- ASSOCIATED PUBLICATION
- RECOMMENDED CITATION
- USEFUL LINKS
- SUPERSPLAT (PREVIEW DATA ON BROWSER)
- ACCESS THE DATASET
- FILE ORGANIZATION
- REPOSITORY LINKS
- FILE LIST
- ADDITIONAL NOTES/COMMENTS
Volumetric Cyclic Immunofluorescence for 3D Spatial Profiling of Immune Structures in Human FFPE Tissue
Alex Y. H. Wong1,2*, Yi Daniel Lu1,2*, Ziyuan Zhao1,2, Felix Zhou3, Hojeong Park4, Zoltan Maliga1,2, Yvonne N. A. Anang5,6, Shannon Coy1,3, Gaudenz Danuser4, Sandro Santagata1,2,6,7, Clarence Yapp1,2† and Peter K. Sorger1,2,7†
1 Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
2 Ludwig Centre at Harvard, Harvard Medical School, Boston, MA, USA
3 Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
4 Broad Institute of MIT and Harvard, Cambridge, MA, USA
5 Tissue Biomarker Laboratory of the Center for Immuno-Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
6 Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
7 Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA, USA
* Authors contributed equally
† Corresponding authors: Clarence Yapp and Peter K. Sorger
Contact: peter_sorger@hms.harvard.edu
This repository accompanies a cyclic light-sheet microscopy study for 3D spatial profiling of immunological structures in human specimens. It is intended to organize analysis resources, dataset access details, and links associated with the manuscript.
Manuscript title: Volumetric Cyclic Immunofluorescence for 3D Spatial Profiling of Immune Structures in Human FFPE Tissue
Publication status: TBD
Journal: TBD
Preprint: https://doi.org/10.64898/2026.05.17.725158
DOI: TBD
Please cite this dataset and repository as:
Wong, A. Y. H. & Lu, Y. et al. (2026). Cyclic Light-sheet Microscopy for 3D Spatial Profiling of Immunological Structures in Human Specimens. {journal / bioRxiv / DOI to be added}.
- Publication DOI:
TBD - Archived record of this repository: https://doi.org/10.5281/zenodo.20170967
- Online data exploration page:
TBD - License / restrictions placed on the data:
TBD
- 20X normal colon: https://superspl.at/scene/b181b113
- virtual H&E: https://superspl.at/scene/44eaf25f
- mature and immature SILTs in normal colon: https://superspl.at/scene/9a6e2550
Dataset access details will be added here as data deposition is finalized. This section can be updated with direct links to image repositories, cloud buckets, portal records, and online viewers.
Add access instructions here once the data hosting location and any access requirements are finalized.
Each file is expected to correspond to a specimen, sample, or derived analysis output. Naming conventions and release locations can be updated here as the dataset is finalized.
| File Type | Description | Location |
|---|---|---|
SampleID.ome.tif |
Stitched cyclic light-sheet image pyramid in OME-TIFF format | TBD |
SampleID-histology.ome.tif |
Histology image of matched or adjacent section, if available | TBD |
SampleID-mask.ome.tif |
Segmentation mask image | TBD |
SampleID-cells.csv |
Single-cell feature table including marker intensities and morphology | TBD |
SampleID-metadata.csv |
Sample- or region-level metadata | TBD |
SampleID-analysis.* |
Downstream analysis outputs and summaries | TBD |
- Zenodo archive: https://doi.org/10.5281/zenodo.20170967
- CyANTs 3D registration workflow: CyANTs README
README.md: Project landing page and dataset information template.CyANTs 3D registration/: ANTsPy-based 3D registration workflow for large multichannel CyCIF / light-sheet Imaris volumes.
- Replace all
TBDentries once the manuscript DOI, data portals, and archive records are available. - Expand the file table with finalized naming conventions and storage locations before public release.