Anne E. Carpenter is an American scientist in the field of image analysis for cell biology and artificial intelligence for drug discovery.

She is the co-creator of CellProfiler, open-source software for high-throughput biological image analysis, and a co-inventor of the Cell Painting assay, a method for image-based profiling.

[2] During this time, she spent a summer in 1996 as an HHMI Undergraduate Research Fellow in the laboratory of Robert E. Malone at the University of Iowa, working on the control of recombination in yeast.

Following her graduation, she spent a summer working on enhancers in Drosophila neural development as a research assistant in the laboratory of Chris Q. Doe, then at the University of Illinois Urbana-Champaign.

There, she developed molecular biology and automated imaging systems to rapidly assess the effects of transcriptional activators on large-scale chromatin structure using fluorescence microscopy.

[3][4][5] Carpenter trained in the laboratory of David M. Sabatini at the Whitehead Institute for Biomedical Research, Cambridge MA, during her postdoctoral work (July 2003 to December 2006).

[6] Using this new tool, she led a team of 5 researchers to develop advanced data mining methods to systematically examine the necessity of proteins for a variety of biological processes.