The Cell Painting Assay (CPA) is a morphological profiling assay where six dyes are used to selectively stain di↵erent cell organelles and compartments, followed by high-content imaging and analysis, generating morphological fingerprints with hundreds of features. CPA is an unbiased assay, that can identify biological activity without requiring a prior target hypothesis, and is therefore particularly well-suited for the screening of new chemical entities of unknown activity. Comparison of the CP profile of a hit molecule with the profiles of reference compounds whose modes of actions and targets are known can then provide target hypotheses, potentially enabling target identification. In our implementation of post-imaging analysis following the feature calculation by the open-source software CellProfiler, 579 Z-scores of morphological features are deduced per compound. The Z-score of a morphological feature represents the di↵erence between a morphological feature and its relative DMSO control. A compound's morphological profile (or simply its CP profile) is thereby a list of its Z-scores. Our processed CP data represents a total of 13450 compounds. In this data, 3114 are reference compounds, whose biological activities are annotated, and 10336 are internal research compounds. The internal research compounds primarily consist of natural products-inspired compounds and pseudo-natural products. 2065 compounds are present in the PhysChem window, and thereby are relevant to this study.