Imaging Mass Cytometry Datasets for Diabetes and Brain Tumors

The diabetes dataset[1] includes human pancreatic tissue profiles from 67 human donors, comprising 33 non-diabetic controls and 34 long-term Type 1 diabetes cases. Each cell was profiled using 38 protein markers, and samples were labeled as either long-duration diabetes or non-diabetic control. Cells were annotated into seven types: T cells, Helper T cells, CD8/Cytotoxic T cells, Neutrophils, Monocytes/Macrophages, general immune cells, and others.

The glioblastoma IMC dataset[2] includes samples from 118 patients (72 glioblastoma and 100 brain metastasis (BrM) tissue regions) after filtering and balancing for common markers. It includes 37 donors per condition, with 21 protein markers profiled. Tissue regions span tumor core, margin, and adjacent normal areas. Cells were annotated into six types: Tc cells, B cells, Astrocytes, M1-like and M2-like MDMs, and undefined cells.

For the data pre-processing, we utilized Cellpose to detect cell centers. After extracting cells from the IMC images, we performed downstream analyses, including cell clustering and cell-type annotation. Cell-type annotation was manually defined at the cluster level rather than on a per-cell basis. Following cell detection, we employed the SLIC algorithm to segment the image into multiple super-pixel regions. This ultimately produced a matrix of cells X protein features within the defined superpixels for subsequent analysis. Each CSV file represents a single IMC sample and contains channel protein data, clinical status, cell type annotations, and various geometric features for each cell.

reference

[1] Nicolas Damond, Stefanie Engler, Vito RT Zanotelli, Denis Schapiro, Clive H Wasserfall, Irina Kusmartseva, Harry S Nick, Fabrizio Thorel, Pedro L Herrera,Mark A Atkinson, et al. 2019. A map of human type 1 diabetes progression by imaging mass cytometry. Cell metabolism, 29(3):755–768.

[2] Elham Karimi, Miranda W Yu, Sarah M Maritan, Lucas JM Perus, Morteza Rezanejad, Mark Sorin, Matthew Dankner, Parvaneh Fallah, Samuel Doré,Dongmei Zuo, et al. 2023. Single-cell spatial immune landscapes of primary and metastatic brain tumours. Nature, 614(7948):555–563.