PTOOL, a suite of tools packaged in an X Window System-based graphical user interface has been developed to allow consistent and accurate selection of single particles from low-contrast spot-scan and flood beam electron microscopy images, These user friendly and computationally efficient tools run on Unix-based workstations. Particles are selected using an automatic reference based selection method which incorporates extensive image preprocessing. An image division and subsequent image sewing mechanism allows for efficient particle selection independent of micrograph size. A particle viewing tool is provided which displays galleries of images and has options for performing image processing operations such as Fourier filtering, histogram equalization, and image masking. In addition, a tool is included to perform semiautomatic focal pair particle matching to identify the same particles on two micrographs. (C) 1996 Academic Press, Inc.