Data used in: “SubCellSpace: Automated characterization of subcellular mRNA localization patterns”
SubCellSpace: Automated characterization of subcellular mRNA localization patterns Author: David Wouters Associated publication: Wouters et al. 2026 (under review) License: Creative Commons Attribution 4.
SubCellSpace: Automated characterization of subcellular mRNA localization patterns
Overview
This repository contains the processed data needed to reproduce the figures and results from Wouters et al. 2026.
File Descriptions
Because Zenodo does not preserve folder structure, files from the original directory tree are listed here with their original paths for reference.
HEK293T Xenium Validation Data
Processed versions of a Xenium spatial transcriptomics experiment on HEK293T cells using an APEX-seq guided gene panel, used to validate whether SubCellSpace can retrieve known subcellular mRNA localization patterns.
| File | Description |
|---|---|
| hek293T_Xenium_adata_subcell_embeddings_classified_and_subtypes.h5ad | Reshaped AnnData object containing just the subcellular embeddings of observations, along with their pattern/no-pattern classifications and pattern subtypes assigned. |
| hek293T_Xenium_adata_subcell_including_randomized_embeddings.h5ad | AnnData object representing the experiment’s count matrix, enriched with another layer containing the SubCellSpace embeddings. Also includes shuffled gene coordinates which are used for pattern-presence testing. |
Small Intestine MERFISH Data
Processed MERFISH spatial transcriptomics data from mouse small intestine, including segmentation masks and staining overlay used for plotting.
| File | Description |
|---|---|
| merfish_SI_adata_subcell_embeddings_classified_and_subtype_and_leiden.h5ad | Reshaped AnnData object containing just the subcellular embeddings of observations, along with their pattern/no-pattern classifications and pattern subtypes assigned. |
| merfish_SI_adata_subcell_including_randomized_embeddings.h5ad | AnnData object representing the experiment’s count matrix, enriched with another layer containing the SubCellSpace embeddings. Also includes shuffled gene coordinates which are used for pattern-presence testing. |
| merfish_SI_polyt_on_dapi_overlay_image.tif | Overlay of DAPI and polyT staining of the MERFISH experiment of a single image tile, used to visualize the enterocyte segmentation. (Original path: stainings/) |
| merfish_SI_segmentation_mask.tif | Mask image file denoting the results of Cellpose segmentation on this specific tile. (Original path: stainings/) |
Simulated Data
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Files are hosted on the source repository. Click download to access the full dataset.