Published January 22, 2024 | Version v2
Dataset Open

Spatial mapping of the hepatocellular carcinoma landscape identifies unique intratumoural perivascular-immune neighbourhoods

Creators

  • 1. ROR icon Centenary Institute
  • 2. ROR icon University of Sydney
  • 3. ROR icon Royal Prince Alfred Hospital
  • 4. ROR icon University of Melbourne

Description

The uploaded data includes results from imaging mass cytometry (IMC) data collected from hepatocellular carcinoma patients. The associated publication can be found here (Marsh-Wakefield et al., 2024, Hepatology Communications).

The CSV file contains segmented cells from IMC data. This includes the Patient, ROI, and Group each cell is assigned. Marker signal intensities underwent arcsine transformation and were rescaled. The “simprof_cluster” column contains the final iteration of clustering following initial X-shift clustering.

Notes on additional columns:

  • “Sample” is barcoded such that the first three digits are the ablation number, followed by the region on the TMA, the group, and the patient. I.e., “[ablation.number]_[TMA.location]_[group]_[patient]”.
  • “x” and “y” refer to the coordinates of samples.
  • “Group” refers to the tissue type. Included non-tumour (NT), invasive margin (IM), and tumour (T) regions.
  • The area for each ROI has been calculated (µm^2 and mm^2).
  • “Batch” refers to TMA.
  • In most cases each area from each patient has three ablation sites. Three samples have an extra ablation site due to technical difficulties during the ablation, and hence have a “split” sample.

The PDF file contains patient information associated with the IMC data.

DOI of dataset:

10.5281/zenodo.10622397

Any further questions can be addressed to Felix Marsh-Wakefield felix.marsh-wakefield@sydney.edu.au

Files

Clinical_details.pdf

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