Four-dimensional imaging: Computer visualization of 3D movements in living specimens

Science

Volumn 273, Issue 5275, 1996, Pages 603-607

  Thomas, C ^a   DeVries, P ^a   Hardin, J ^a   White, J ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER PROGRAM; COMPUTER SIMULATION; COMPUTER SYSTEM; IMAGE ANALYSIS; IMAGE PROCESSING; INFORMATION PROCESSING; MICROSCOPY; PRIORITY JOURNAL; REVIEW;

EID: 0029750188     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.273.5275.603     Document Type: Review

References (16)

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10. A. Fire [Comput. Appl. Biosci. 10, 443 (1994)] describes a 4D system implemented on an IBM PC-compatible computer.
11. The 4D live cell imaging workstation at IMR uses the following hardware; however, many combinations of hardware may be used for 4D imaging, and this list is neither a recommendation of what to buy nor an indication of what is necessary to do this type of data collection. Microscope: Nikon Diaphot 200 with Nomarski optics and a Nikon oil immersion lens (100X, numerical aperture 1.4). Video camera: Sierra Scientific Video Standard LSV-1 Vidicon with Nikon zoom lens (0.75X to 2.5X). Image processor: Dage DSP-2000. Frame grabber: Scion LG 3. Focus drive: ASI model 85. Shutter drive: ASI SC-2 shutter controller (the Ludl MAC 1000 and MAC 2000 systems are also supported). Computer: Macintosh Quadra 950, PPC upgrade card, 25 megabytes of RAM, 1-gigabyte internal hard drive, 1.2-gigabyte APS magnetooptical drive (for archival purposes). Recently, a second system has been set up with a Macintosh 7600/ 120 computer and a Scion AG 5 frame grabber. The AG 5 frame grabber can perform frame averaging, thereby obviatina the need for a separate image processor.
12. The 4D Acquisition software is based on NIH Image, a popular shareware image processing program, and is basically an extensive set of control macros for NIH Image that allows the user to configure and control the image acquisition conditions through a series of graphic user interfaces. The NIH Image program is a freely available general-purpose image processing system for Macintosh computers. It features a comprehensive macro language that was used to implement the data capture commands of the system. A user can easily extend or customize his or her acquisition software by editing and modifying the macros. NIH Image was written and is maintained by W. Rasband. Executable code and associated documentation can be obtained from the NIH Image World Wide Web site, http://rsb.info.nih. gov/nih-image/.
13. We found that we could obtain up to 25% more data compression and better final image quality if we filtered out residual electronic or photon noise from the images. For Nomarski imaging, we use a four-frame running-average filter implemented on a Dage DSP 2000 image processor. On another system, we use a four-frame average on a Scion AG 5 integrating frame grabber, thereby obviating the need for a separate image processor.
14. IMR's 4D Acquisition software, 4D Turnaround program, 4D Viewer program, and the related documentation are available by anonymous FTP from: Address: ftp2.bocklabs.wisc.edu User name: anonymous Password: your e-mail address Directory: pub/lmb/imr/4D_Viewer Folders: "Acquisition Macros," "Turnaround," and "Viewer," respectively Alternatively, the software can be downloaded from IMR's Web site, http://www.bocklabs.wisc.edu/ imr/imr.html. This site also contains further information on 4D microscopy, including equipment purchase considerations, vendor addresses, and equipment costs. If you wish to be put on a list to receive information about future upgrades or releases of IMR's 4D software, send an e-mail outlining your request to cfthoma1@facs:aff.wisc.edu with your name, mailing address, and phone number. Note that turning around large data sets can be time-consuming. On a Macintosh 8500, the 4D Turnaround program will process 10 time points consisting of 20 focal planes of images of 300 by 400 pixels in ∼ 1.5 min.
15. J. E. Sulston, E. Schierenberg, J. G. White, J. N. Thomson, Dev. Biol. 78, 64 (1983).
16. We thank V. Centonze for ongoing support and discussions, V. Centonze and C. Lavin for constructive comments on the manuscript, D. Wokosin for setting up the instrumentation, W. Russin for the Elodea sample shown in Fig. 3, and the users of the system for their suggestions for improvements and identification of bugs. Supported by NIH grant P41-RR00570-26.