Xcyt for Linux version 1.0 1) INSTALLING $ gunzip distrib.tar.z $ tar xvf distrib.tar That's it! Make sure that the directory where you put these files appears in your executable path. 2) RUNNING $ xcyt where is the name of a 640x400, gray-scale Targa file (can be compressed), with no extension. So, for instance, if you have a compressed image called new_case.tga.Z, you simply type $ xcyt new_case You can also specify a directory path on the command line, e.g., $ xcyt ../images/new_case Note that xcyt is just a bash script that provides an interface to the Xcyt executable. You can change this script if the details of your implementation are different than mine. (The image conversion programs tgatoppm and ppmtopgm are part of the netpbm package, freely available at different places on the Net. Let me know if you choose to use a different image format and we can work out the conversion details.) **Important Note** The cytological feature values computed by Xcyt are saved to a file called cell.data. This file can, under rare circumstances, become corrupted. I strongly recommend that, as you are working, you occasionally (say, every 10 or 20 images) copy (or move) cell.data to another file, to make sure that your work is not lost. The colormap handling is not very good. If you have false colors appearing on the image, you may have to kill other color-hogging applications that you are running, and re-start Xcyt. 3) XCYT OPERATION click left mouse button to begin outlining nucleus click left mouse button again to stop outlining & fill in the initial boundary click right mouse button to run all unconverged snakes click middle mouse button to delete closest snake (if you have a 2-button mouse, click both simultaneously to delete) The buttons should be self-explanatory. Keep in mind that the "features" button not only computes feature values but also writes the results to the cell.data file. The "diagnosis" and "prognosis" buttons then read that file to get their information. Note that features are computed for all outlined nuclei, even if the snake has not been run to convergence. 4) BUG REPORTING Please let me know any bugs that you may find, or any comments or questions about the operation of this program. Nick Street street@cs.wisc.edu