Example imaging mass cytometry raw data

This imaging mass cytometry (IMC) dataset serves as an example to demonstrate raw data processing and downstream analysis tools. The data was generated as part of the <strong>I</strong>ntegrated i<strong>MMU</strong>noprofiling of large adaptive <strong>CAN</strong>cer patient cohorts (IMMUcan) project (immucan.eu) using the Hyperion imaging system (www.fluidigm.com/products-services/instruments/hyperion). To get an overview on the technology and available analysis strategies, please visit bodenmillergroup.github.io/IMCWorkflow. The individual data files are described below: <strong>Patient1.zip, Patient2.zip, Patient3.zip, Patient4.zip</strong>: raw data files of 4 patient samples. Each .zip archive contains a folder in which one .mcd file (IMC raw data) and multiple .txt files (one per acquisition) can be found. <strong>compensation.zip</strong>: This .zip archive holds a folder which contains one .mcd file and multiple .txt files. Multiple spots of a "spillover slide" were acquired and each .txt file is named based on the spotted metal. This data is used for channel spillover correction. For more information, please refer to the original publication: Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry <strong>panel.csv</strong>: This file contains metadata for each antibody/channel used in the experiment. The <em>full</em> column indicates which channel should be analysed. The <em>ilastik</em> column specifies which channels were used for ilastik pixel classification and the <em>deepcell</em> column indicates the channels used for deepcell segmentation. <strong>sample_metadata.csv</strong>: This file links each patient to their cancer type (SCCHN - head and neck cancer; BCC - breast cancer; NSCLC - lung cancer; CRC - colorectal cancer).本成像质谱流式（imaging mass cytometry, IMC）数据集作为示例，用于演示原始数据处理与下游分析工具的使用方法。本数据集源自大型癌症患者队列整合免疫 profiling（IMMUcan）项目（官网：immucan.eu），使用Hyperion成像系统（www.fluidigm.com/products-services/instruments/hyperion）生成。若需了解该技术与可用分析策略的概览，请访问：bodenmillergroup.github.io/IMCWorkflow。 各数据文件说明如下： **Patient1.zip、Patient2.zip、Patient3.zip、Patient4.zip**：4份患者样本的原始数据文件。每个压缩包均包含一个文件夹，内含1个.mcd文件（IMC原始数据）与多个.txt文件（每次采集对应1个.txt文件）。 **compensation.zip**：该压缩包内含一个文件夹，内有1个.mcd文件与多个.txt文件。研究人员采集了“溢漏玻片”的多个位点数据，每个.txt文件均根据所标记的金属元素命名。此数据集用于通道信号溢漏校正。如需更多信息，请参阅原始文献：《Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry》（悬浮与成像质谱流式的信号溢漏校正）。 **panel.csv**：本文件包含实验中所用的每种抗体/通道的元数据。其中*full*列标注需进行分析的通道；*ilastik*列指定用于ilastik像素分类的通道；*deepcell*列标注用于deepcell分割的通道。 **sample_metadata.csv**：本文件将每位患者与其对应的癌症类型进行关联（SCCHN：头颈部癌；BCC：乳腺癌；NSCLC：肺癌；CRC：结直肠癌）。