Programs for Acquisition & Analysis of 4d Microscopy Data Sets

Abstract

The goal of this project is to develop a suit of software programs that will nllow for the capture and analysis of multiple focal-plane, time-lapse movies. The acquisition of 3-dimensional time-lapse (4D) data sets involves the precise orchestration of a variety of hardware components including z-focus control motors, illumination shutters, digitizing video framegrabbers, serial I/O ports, etc. (Thomas et al. (1996) Science, 273, 603-607, Thomas dc White (1996) Sci. Comp. World, 24, 31-32). In the past, the IMR's 4D Live Cell Microscopy program has relied on an elaborate set of control macros for the freeware image processing application """"""""NlH-Image"""""""" to perform 4D data acquisition. While it deDmitely provided a usable system, the problem with this strategy was that NIH-Image macros are limited to 32 kb in size. The IMR's 4D acquisition macros quickly reached, and then exceeded this limit. Adding new features to the software or supporting new hardware components meant removing existing features or support. The goal of this subproject was to develop a non-dependent stand-alone Macintosh application for the acquisition of 4D data sets which would be unlimited in the amount of features that could be added and the number of hardware components which could be supported. It was also hoped that by optimizing the software specifically for 4D acquisition, that improvements in acquisition speed and ease-of-use would also be realized. The result of this project, the """"""""4D Grabber"""""""" application, is a significant step forward in 4D acquisition technology. Not only does the """"""""4D Grabber"""""""" application seamlessly coordinate the various hardware components of a 4D Live Cell microscopy workstation, but does so using easy to-understand graphic user interfaces in order to reduce the learning curve for the researcher wishing to perform these types of experiments in their own labs. The software supports 6 common digitizing framegrabber cards of both the Nubus and PCI slot configuration (including the ability to take advantage of on-card frame averaging, if present), and supports four different stage drive motors. Its modular code design makes adding support for additional hardware systems very straightforward. Significant increases in collection speed were also realized with the software's optimized design. An additional advantage of the """"""""4D Grabber"""""""" software is the ability to gather 4D data directly to compressed QuickTime movies. By taking advantage of this feature, it is possible to gather up to 15 times as many data points per given hard disk space than when using previous 4D collection systems. This collection mode also offers a very impressive savings in time since the lengthy data translation stage (which was formerly necessitated with all 4D data sets) can be completely eliminated. This application, like all the others in the IMR's 4D Imaging Suite, will be available free-of-charge to researchers all over the world via downloading from the Internet.

Funding Agency

• Agency: National Institute of Health (NIH)
• Institute: National Center for Research Resources (NCRR)
• Type: Biotechnology Resource Grants (P41)
• Project #: 3P41RR000570-27S1
• Application #: 2757603
• Budget Start: 1997-10-01
• Budget End: 1998-09-30
• Support Year: 27
• Fiscal Year: 1998

Institution

• Name: University of Wisconsin Madison
• DUNS #: 161202122
• City: Madison
• State: WI
• Country: United States
• Zip Code: 53715

Publications

Malecki, Marek; Putzer, Emily; Sabo, Chelsea et al. (2014) Directed cardiomyogenesis of autologous human induced pluripotent stem cells recruited to infarcted myocardium with bioengineered antibodies. Mol Cell Ther 2:

Malecki, Marek (2014) 'Above all, do no harm': safeguarding pluripotent stem cell therapy against iatrogenic tumorigenesis. Stem Cell Res Ther 5:73

Mavroudi, Maria; Zarogoulidis, Paul; Porpodis, Konstantinos et al. (2014) Stem cells' guided gene therapy of cancer: New frontier in personalized and targeted therapy. J Cancer Res Ther (Manch) 2:22-33

Malecki, Marek; LaVanne, Christine; Alhambra, Dominique et al. (2013) Safeguarding Stem Cell-Based Regenerative Therapy against Iatrogenic Cancerogenesis: Transgenic Expression of DNASE1, DNASE1L3, DNASE2, DFFB Controlled By POLA1 Promoter in Proliferating and Directed Differentiation Resisting Human Autologous Pluripotent J Stem Cell Res Ther Suppl 9:

Malecki, Marek; Tombokan, Xenia; Anderson, Mark et al. (2013) TRA-1-60(+), SSEA-4(+), POU5F1(+), SOX2(+), NANOG(+) Clones of Pluripotent Stem Cells in the Embryonal Carcinomas of the Testes. J Stem Cell Res Ther 3:

Malecki, Marek (2013) Improved targeting and enhanced retention of the human, autologous, fibroblast-derived, induced, pluripotent stem cells to the sarcomeres of the infarcted myocardium with the aid of the bioengineered, heterospecific, tetravalent antibodies. J Stem Cell Res Ther 3:

Malecki, Marek; Dahlke, Jessica; Haig, Melissa et al. (2013) Eradication of Human Ovarian Cancer Cells by Transgenic Expression of Recombinant DNASE1, DNASE1L3, DNASE2, and DFFB Controlled by EGFR Promoter: Novel Strategy for Targeted Therapy of Cancer. J Genet Syndr Gene Ther 4:152

Zarogoulidis, Paul; Darwiche, Kaid; Sakkas, Antonios et al. (2013) Suicide Gene Therapy for Cancer - Current Strategies. J Genet Syndr Gene Ther 4:

Malecki, Marek; Sabo, Chelsea; Putzer, Emily et al. (2013) Recruitment and retention of human autologous CD34+ CD117+ CD133+ bone marrow stem cells to infarcted myocardium followed by directed vasculogenesis: Novel strategy for cardiac regeneration. Mol Cell Ther 1:

Malecki, Marek; Malecki, Bianca (2012) Nuclear routing networks span between nuclear pore complexes and genomic DNA to guide nucleoplasmic trafficking of biomolecules. J Fertili In Vitro 2: