In January 2007, Carpenter founded her laboratory at the
Broad Institute of Harvard and MIT, as the Director of the Imaging Platform. Her first
NIH R01 grant was awarded in 2010, at the age of 33. In 2017, she became a Broad Institute Scientist. The Carpenter group develops novel strategies and tools to analyse biological images, particularly microscopy images from high-throughput experiments. Her
computer scientists and
biologists develop free
open-source image analysis and data exploration methods such as
CellProfiler and CellProfiler Analyst. Their software work has contributed to open source applications and libraries, including
ImageJ,
TensorFlow,
scikit-image, and
scikit-learn. The lab collaborates with biologists, generating discoveries across fields of study and disease areas. Their software enables
high-throughput screening in challenging model systems such as
C. elegans, 3D cell cultures, and time-lapse video of growing cells. The focus of the Carpenter lab turned towards
machine learning by 2009, and later
deep learning, to identify biological structures of interest and to identify patterns resulting from chemical or genetic perturbations to identify cures for diseases. She was an early pioneer of the new field of image-based profiling, which is related to
gene expression profiling but uses microscopy images as the data source. Together with
Stuart Schreiber, the Carpenter laboratory invented the
Cell Painting assay, which is the most widely used for this purpose. Carpenter's CellProfiler software and Cell Painting assay formed the initial scientific platform for Recursion Pharmaceuticals. Dr. Carpenter is a member of the Scientific and Technical Advisory Board for Recursion Pharmaceuticals, in addition to that of
Bio-Rad Laboratories. Carpenter has given more than 200 invited lectures and has chaired several
conferences and workshops. She has authored over 200 scientific publications as of 2022. She is known for efforts that organize the scientific community: she was an early Board member for the Society for Biomolecular Imaging and Informatics (SBI2), she founded the CytoData Society, and she led the 2018 Data Science Bowl via Kaggle. Since 2007, Carpenter has supervised over 70 researchers and students, from
postdoctoral to high-school level and is known for her informal mentoring as well. In 2021, Dr. Shantanu Singh became co-leader of Carpenter's laboratory, now called the CarpenterSingh lab. == Awards and honors ==