Processed Multiplexed Ion Beam Imaging (MIBI) of tumor microenvironments of 54 melanoma samples following immunotherapy
Description
This dataset consists of processed results from a MIBI (Multiplexed Ion Beam Imaging) study of 54 patients with melanoma who received immunotherapy. MIBI is a highly multiplexed imaging technique that enables the simultaneous, quantitative detection of dozens of protein markers within tissue samples at sub-cellular resolution. It combines antibody-based staining with time-of-flight secondary ion mass spectrometry (ToF-SIMS) to analyze the tumor microenvironment. The 29-protein panel used in this MIBI study included markers for broad cell typing (e.g., CD45, SOX10), myeloid subsets (CD68, CD163), lymphocyte subsets (CD3, CD8), immune checkpoints (PD-1, PD-L1, LAG-3, TIM-3), and other markers (e.g., proliferation, structural markers). After imaging on field of view (FOV) for each patient sample, the arcsinh-transformed values of the panel proteins were used in conjunction with a deep learning-based object-detection model (trained on previously segmented MIBI studies) to localize and classify the cell types within each FOV. The 'scaled_mibi_data_w_cell_gating.csv' file contains these results, where each row is for one cell identified in an FOV. This table includes cells' spatial information (x and y-coordinates and estimated area), their 29 arcsinh-transformed protein intensity measurements, and boolean columns for their cell typing. Note that these cell types are hierarchical, falling under four main categories: tumor cells, fibroblasts, smooth muscle/myofibroblasts, and immune cells. In addition, the 'patient_info.csv' file contains some basic (non-identifying) patient characteristics (age tertile at diagnosis within the 54 patient sample, and Roman numeral stage at diagnosis), along with two clinical outcome variables: 'response_binary' and 'response_multi'. Specifically, a value of 1 in the 'response_binary' variable indicates whether the patient showed stable disease, a partial response, or remission after immunotherapy (0 then represents progressive disease); the 'response_multi' variable encodes their more granular outcome (CR = complete response, PR = partial response, SD = stable disease, PD = progressive disease).