Free Flow Cytometry Software Detailed Description Form (form revised 2/2/95) ---------------------------------------------------------------------- **SECTIONS** The sections of this form are: **SHORT OVERVIEW** **BASICS** **DOCUMENTATION** **INPUT/OUTPUT** **DOT PLOTS** **CONTOUR & DENSITY PLOTS** **HISTOGRAMS** **KINETICS** **CELL CYCLE ANALYSIS** **TECHNICAL MATTERS** **COMMENTS/SPECIAL FEATURES** ---------------------------------------------------------------------- **SHORT OVERVIEW** (Paragraph of not more than 10 lines) ---------------------------------------------------------------------- **BASICS** Name of program: ANALYSE Date this form was completed/revised:19 february 1995 Computer operating systems supported (if MS-DOS, does the program require Windows?): MS-DOS, does NOT require Windows. Author(s) of program, contact addresses and phone numbers: Tom Bakker Schut, Richard Doornbos and Bart de Grooth(*): Technical optics group, Dept. of Applied Physics, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands. Tel.no. : -31-53-893157 Fax.no. : -31-53-309549 E-mail : top@eltn.utwente.nl Telex : 44200 (*): Author to whom all correspondence should be sent. Where/how to get the program: ftp: marlin.bio.umass.edu: /pub/flowcyt/autoklus. ---------------------------------------------------------------------- **DOCUMENTATION** On-line help: only small amounts. Is there a tutorial? If so, length? Major topics covered? No tutorial. Are sample data files provided with the tutorial? N/A Manual, other documentation or published reference: Comp Biomed Res 27:83-96, 1994. ---------------------------------------------------------------------- **INPUT/OUTPUT** Input data file formats accepted: FCS1.0, FCS2.0 Video screen types supported:EGA/VGA Printers and other output devices supported: HP Paintjet only. Output disk file types created (if any): *.win : windowsettings *.anu : usersettings *.hp# : histogram output of paramter # (text) celcoll.arr, data.ar: temporary data storage Mouse control: Yes. ---------------------------------------------------------------------- **DOT PLOTS** Can dot plots be displayed? Yes. Can multiple dot plots be displayed on the screen simultaneously? Yes, two screens of 6 each. Dot plot regions (polygonal, rectangular, elliptical, etc.): Polygonal regions can be drawn. Gating logic options for regions: 5 * 3 AND-gates for one population, 14 defined populations max + 1 undefined . Are dots in different regions colored differently? If yes, do these colors carry over into dot plots of different parameters? Yes. 3D dotplots? If yes, can they be rotated and tilted to any desired angle? Yes, no. Is quadrant analysis supported? If yes, can the results be shown on the dotplot itself? No. ---------------------------------------------------------------------- **CONTOUR & DENSITY PLOTS** 2D contour plots? If yes, with colored contour lines? Smoothable? Yes, no, no. 3D contour plots? If yes, with rotation and tilting? Smoothable? No. Can density plots be displayed? If yes, in color? Smoothable? Yes, yes, no. ---------------------------------------------------------------------- **HISTOGRAMS** Are medians/means for log acquired data converted to a linear intensity scale? No. Can arbitrary markers be placed on histograms to give percentages and medians/means? No. What statistics are available for marked segments? None. Can statistics for a marked segment be shown on the histogram itself? No. Can histograms be filled solid with a user-selected color? No. Is smoothing available? If yes, which algorithms, and can user specify number of cycles? Yes, see lit. ref. for algorithm, yes. Can histograms be overlayed (maximum number per panel): Yes, 14. Histogram/overlay vertical scaling options: Choice between absolute and relative scaling for different populations (relative to population maximum). Overlayed histogram lines: can different colors be used? If yes, can user select colors? Yes, no. Overlayed histogram lines: can thickness, dotted/broken be selected? No. Can histograms be displayed as a 3D arrangement? If yes, can the display be rotated and tilted? No. ---------------------------------------------------------------------- **KINETICS** Are dots on dotplots sampled evenly throughout the listmode file? All dots shown, no sampling. Can time be used as a region/gating parameter? Not time but order of measurement can be used. Can the median Y line be drawn vs. time? No. Can event number be used as a dotplot X parameter if time is not a recorded parameter? Yes. Can medians be obtained for a user-specified number of slices of each listmode file? Yes. ---------------------------------------------------------------------- **CELL CYCLE ANALYSIS** Is cell cycle analysis of DNA fluorescence histograms supported? No. Models/algorithms available: None. ---------------------------------------------------------------------- **TECHNICAL MATTERS** Program configuration information saved between sessions: Yes. Computer requirements (memory, video display, floating point hardware, etc.): PC 286 (AT) and higher, no drivers in base memory, preferably Ram-disk installed (for speed). Source code programming language used, interpreters required (if any), approx. total lines of source code: Turbo Pascal, ca. 16000 lines (all code included) Compiler manufacturer and version: Borland Turbo Pascal 6.0. Commercial libraries or development tools required to produce the executable program from the free source code? Yes, TurboPowerSoftware Seconds required to read/process a 10,000 event, 5-parameter file (specify computer system[s] used for timing): About 10-15 seconds on 40 MHz 486 (with Ram disk) to read and display 10.000 events. ---------------------------------------------------------------------- **COMMENTS/SPECIAL FEATURES** - creation of new paramters by transformation and division. - batch-options for automatic gating and plotting using predefined windows. - no more help available, development is stopped. ---------------------------------------------------------------------- [END OF FORM] ----------------------------------------------------------------------