Xenium In Situ Spatial Transcriptomics for Two HCC Samples

17.8 GB of raw Xenium spatial transcriptomics output for two hepatocellular carcinoma (HCC) samples, M293 and M316, profiled with a custom gene panel. The dataset includes transcripts files in Parquet and Zarr formats and morphology images in OME-TIF format. It was uploaded by Narein Rao on figshare and last updated on May 5, 2026.

Use Cases

• Develop spatial gene expression analysis pipelines based on the provided transcripts data.
• Train models for cell segmentation or tissue morphology analysis based on the OME-TIF images.
• Benchmark custom gene panel performance in HCC samples based on the spatial transcriptomics output.
• Integrate transcript location data with cellular morphology for multi-modal spatial analysis.

Strengths

• Dataset size of 17.8 GB indicates a substantial volume of raw spatial transcriptomics data.
• Includes both quantitative transcript data (Parquet/Zarr) and high-resolution morphology images (OME-TIF), enabling multimodal analysis.
• Data is from a specific, clinically relevant context: two hepatocellular carcinoma (HCC) samples.

Limitations

• Row count and specific column definitions are unknown, which limits suitability assessment for specific analytical tasks.
• Description metadata is limited; actual data structure and quality require manual inspection after download.

Provenance

Source

figshare

Collection Method

Profiled using a Xenium Analyzer machine with a custom gene panel.

Freshness

Last updated 2026-05-05 22:40:55; freshness should be verified.