Thouis "Ray" Jones

Biologists can now prepare and image thousands of samples per day using automation, enabling chemical screens and functional genomics (for example, using RNA interference). Here we describe the first free, open-source system designed for flexible, high-throughput cell image analysis, CellProfiler (www.cellprofiler.org). CellProfiler can address a variety of biological questions quantitatively, including standard assays (for example, cell count, size, per-cell protein levels) and complex morphological assays (for example, cell/organelle shape or subcellular patterns of DNA or protein staining).

Visual inspection of cells is a fundamental tool for discovery in biological science. Modern robotic microscopes are able to capture thousands of images from massively parallel experiments such as RNA interference (RNAi) or small-molecule screens. Such screens also benefit from lab automation, making large screens, e.g., genome-scale knockdown experiments, more feasible and common. As such, the bottleneck in large, image-based screens has shifted to visual inspection and scoring by experts.

In this paper, we describe the methods we have developed for automatic image cytometry. The paper demonstrates illumination normalization, foreground/background separation, cell segmentation, and shows the benefits of using a large number of individual cell measurements when exploring data from high-throughput screens.

We present a method for finding the boundaries between adjacent regions in an image, where seed areas have already been identified in the individual regions to be segmented. This method was motivated by the problem of finding the borders of cells in microscopy images, given a labelling of the nuclei in the images. The method finds the Voronoi region of each seed on a manifold with a metric controlled by local image properties. We discuss similarities to other methods based on image-controlled metrics, such as Geodesic Active Contours, and give a fast algorithm for computing the Voronoi regions. We validate our method against hand-traced boundaries for cell images.