CellProfiler Analyst (CPA) provides tools for classifying biological images and exploring and visualizing multidimensional data (particularly from high-throughput experiments) that has been extracted from companion image analysis software CellProfiler.

CellProfiler Analyst’s primary tools:

  • Image Gallery displays (full and cell) images with a variety of filter options and can be used interactively with other tools.
  • Classifier enables cell and field-of-view-level classification of multiple phenotypes using popular supervised machine learning models.
  • Plate Viewer displays data according to the spatial layout of the experiment, such as a multi-well plate or microarray.
  • Scatter Plot, Histogram, and Density Plot display numerical data.
  • Table Viewer displays numerical and text data in a spreadsheet format, where data points can be clicked to display images.
  • Normalization Tool creates a new datatable with normalized and feature-selected columns.

The CellProfiler project is based at the Broad Institute Imaging Platform. It was started by Anne E. Carpenter and Thouis (Ray) Jones in the laboratories of David M. Sabatini and Polina Golland at the Whitehead Institute for Biomedical Research and MIT’s CSAIL. David Dao currently leads the development of CellProfiler Analyst. CellProfiler Analyst is tested on MacOS 10.10 and 10.11, Windows 7 and 10, and to a lesser extent Linux. Running the software from Linux currently requires use of the source code, which is beyond the scope of this document.

CellProfiler Analyst is distributed under the BSD-3 Clause (see LICENSE.txt).