A computational workflow for cell line profiling by Imaging Mass Cytometry.

Imaging Mass Cytometry Data as 32-bit single TIFF with computational analysis from the manuscript: A computational workflow for cell line profiling by Imaging Mass Cytometry. Breast cancer cell lines SKBR3 MCF7 HCC1143 IMC data and CellProfiler pipelines.zip Elongated cell lines HeLa SKOV3 BJ IMC data and CellProfiler pipelines.zip: Small cell lines A431 HT29 BxPC3 IMC data and CellProfiler pipelines.zip U937 PMA-differentiated cells IMC data and CellProfiler pipeline.zip A431 Cisplatin Study IMC data and CellProfiler pipeline.zip Contains 1 folder per cell line or drug treatment of single TIFF 32-bit markers exported from MCD/txt files (including Xe131 channel) and their respective cpproj. pipeline file for IMC Cell Line Profiler workstream reproducible analysis IMC Cell Line Profiler high dimensional and correlation analysis R scripts.zip Contains three adaptable R scripts for high dimensional analysis, correlation analysis and combination of both scripts for Machine Learning classified datasets. Breast cancer cell lines nuclear state classification by CellProfiler Analyst MLs.zip Contains SQLite databases, properties files, training datasets, nuclear classes visual rendering, and classifier model files with outputs for two machine learning classifiers (Random Forest and Fast Gentle Boosting) per breast cancer cell line for CellProfiler Analyst workflow reproducibility. A431 Cisplatin Study IMC data nuclear state classification by CellProfiler Analyst MLs.zip Contains SQLite databases, properties files, training datasets, classifier model with outputs for Fast Gentle Boosting and Random Forest per treatment for CellProfiler Analyst workflow reproducibility. IMC Cell Line Profiler pseudo-color images with Ki-67 marker Cytoplasm marker and Cell-ID nuclei (Fig2 Fig3), visual nuclei and whole-cell segmentation contours rendered images (Fig4). Non-compensated and compensated multiTIFF 32-bit cells lines with Cellprofiler masks SCE objects and FCS files and Datatables.zip Contains publicly available compensation matrix (https://zenodo.org/records/7575859) , R compensation script (Compensation IMC data with CATALYST.R), compensated and non-compensated multiTIFF stacks 32-bit per cell line experiment, exported CellProfiler 16-bit masks per cell line dataset, R single cell experiment script (Conversion IMC data to Single Cell Experiments Objects and FCS.R) with inputs and outputs (fcs files, sce files, panel files, metadata files),R conversion single cell experiment to datatable script (Conversion SCE to Datatable and analysis.R). Step-by-step guide to assist users with the IMC Cell Line Profiler computational workflow.本数据集为采用32位单帧TIFF格式存储的成像质谱流式细胞术（Imaging Mass Cytometry, IMC）数据，配套对应论文《A computational workflow for cell line profiling by Imaging Mass Cytometry》的计算分析流程。 乳腺癌细胞系SKBR3、MCF7、HCC1143的IMC数据及CellProfiler分析流程.zip 拉长型细胞系HeLa、SKOV3、BJ的IMC数据及CellProfiler分析流程.zip 小型细胞系A431、HT29、BxPC3的IMC数据及CellProfiler分析流程.zip U937经PMA诱导分化的细胞IMC数据及CellProfiler分析流程.zip A431顺铂处理研究的IMC数据及CellProfiler分析流程.zip 每个细胞系或药物处理组对应一个独立文件夹，内含从MCD/txt格式文件导出的32位单帧TIFF标记图像（包含Xe131通道），以及用于IMC细胞系表征工作流可重复分析的对应cpproj格式分析流程文件。 IMC细胞系表征高维分析与相关性分析R脚本.zip 内含3个可适配的R脚本，分别用于高维数据分析、相关性分析，以及二者结合的机器学习分类数据集分析流程。 基于CellProfiler Analyst机器学习模型的乳腺癌细胞系细胞核状态分类数据集.zip 内含SQLite数据库、属性文件、训练数据集、细胞核类别可视化渲染文件，以及针对每个乳腺癌细胞系的两种机器学习分类器（随机森林（Random Forest）与快速温和提升（Fast Gentle Boosting））的分类器模型文件及输出结果，用于复现CellProfiler Analyst工作流。 A431顺铂处理研究的IMC数据细胞核状态分类CellProfiler Analyst机器学习模型数据集.zip 内含SQLite数据库、属性文件、训练数据集、针对每个处理组的快速温和提升与随机森林分类器模型及输出结果，用于复现CellProfiler Analyst工作流。 IMC细胞系表征伪彩色图像数据集：包含Ki-67标记物、细胞质标记物与Cell-ID细胞核标记（对应图2、图3），以及可视化细胞核与全细胞分割轮廓的渲染图像（对应图4） 含CellProfiler掩膜、单细胞实验（Single Cell Experiment, SCE）对象、FCS文件与数据表的未补偿及已补偿32位多帧TIFF细胞系数据.zip 内含公开可用的补偿矩阵（来源：https://zenodo.org/records/7575859）、R语言补偿脚本《Compensation IMC data with CATALYST.R》、每个细胞系实验对应的32位已补偿与未补偿多帧TIFF图像栈、每个细胞系数据集导出的16位CellProfiler掩膜文件、用于将IMC数据转换为单细胞实验对象与FCS文件的R脚本《Conversion IMC data to Single Cell Experiments Objects and FCS.R》（含输入输出文件：fcs文件、sce文件、panel文件、元数据文件），以及将单细胞实验对象转换为数据表并进行分析的R脚本《Conversion SCE to Datatable and analysis.R》。 配套分步操作指南，协助用户完成IMC细胞系表征计算工作流。