Introduction

In our paper, we used a human metastatic lymph node sample to benchmark the reproducibility and efficiency of Open-ST for 3D reconstruction.

We profiled patient-matched samples from human head and neck squamous cell carcinoma (HNSCC), due to the interesting transcriptional diversity and spatial organization. For the human metastatic lymph node, we applied Open-ST to serial sections spanning 350 μm. We constructed a 3D virtual tissue block with over a million cells and hundreds of millions of transcripts embedded in the H&E stainings.

In the following sections, we explore how to reproduce the (pre)processing for these data.

These steps are introduced in our STAR Protocols paper. The data is described in our Open-ST paper, in Cell.