Fig. 1: SPACe workflow and performance on JUMP MOA reference datasets.
From: SPACe: an open-source, single-cell analysis of Cell Painting data
A A graphical depiction of the steps included in the SPACe pipeline. B Example of four SPACe segmented objects (out of thousands of images) in CP-stained U-2 OS cells, please note that the fifth compartment (cytoplasm) is obtained by subtraction of the nuclear mask from the cell mask. Scale bar: 5 µm. C Processing time for JUMP MoA reference datasets using either CellProfiler or SPACe, each symbol represents running time for a plate of the reference dataset, with also the mean ± standard deviation overlayed. D Assessment of percent replicating (top) and percent matching (bottom) based on population mean (CellProfiler, SPACe) or EMD (SPACe only). Assessment of analysis feature percent replicating (E) or percent matching (F) by the mechanisms of actions present in the JUMP reference datasets. Source data are provided as a Source Data file.
