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.