11 research outputs found
Reproducible image-based profiling with Pycytominer
Technological advances in high-throughput microscopy have facilitated the
acquisition of cell images at a rapid pace, and data pipelines can now extract
and process thousands of image-based features from microscopy images. These
features represent valuable single-cell phenotypes that contain information
about cell state and biological processes. The use of these features for
biological discovery is known as image-based or morphological profiling.
However, these raw features need processing before use and image-based
profiling lacks scalable and reproducible open-source software. Inconsistent
processing across studies makes it difficult to compare datasets and processing
steps, further delaying the development of optimal pipelines, methods, and
analyses. To address these issues, we present Pycytominer, an open-source
software package with a vibrant community that establishes an image-based
profiling standard. Pycytominer has a simple, user-friendly Application
Programming Interface (API) that implements image-based profiling functions for
processing high-dimensional morphological features extracted from microscopy
images of cells. Establishing Pycytominer as a standard image-based profiling
toolkit ensures consistent data processing pipelines with data provenance,
therefore minimizing potential inconsistencies and enabling researchers to
confidently derive accurate conclusions and discover novel insights from their
data, thus driving progress in our field.Comment: 13 pages, 4 figure