A 2D/3D image analysis system to track fluorescently labeled structures in rod-shaped cells: application to measure spindle pole asymmetry during mitosis.

BACKGROUND: The yeast Schizosaccharomyces pombe is frequently used as a model for studying the cell cycle. The cells are rod-shaped and divide by medial fission. The process of cell division, or cytokinesis, is controlled by a network of signaling proteins called the Septation Initiation Network (SIN); SIN proteins associate with the SPBs during nuclear division (mitosis). Some SIN proteins associate with both SPBs early in mitosis, and then display strongly asymmetric signal intensity at the SPBs in late mitosis, just before cytokinesis. This asymmetry is thought to be important for correct regulation of SIN signaling, and coordination of cytokinesis and mitosis. In order to study the dynamics of organelles or large protein complexes such as the spindle pole body (SPB), which have been labeled with a fluorescent protein tag in living cells, a number of the image analysis problems must be solved; the cell outline must be detected automatically, and the position and signal intensity associated with the structures of interest within the cell must be determined. RESULTS: We present a new 2D and 3D image analysis system that permits versatile and robust analysis of motile, fluorescently labeled structures in rod-shaped cells. We have designed an image analysis system that we have implemented as a user-friendly software package allowing the fast and robust image-analysis of large numbers of rod-shaped cells. We have developed new robust algorithms, which we combined with existing methodologies to facilitate fast and accurate analysis. Our software permits the detection and segmentation of rod-shaped cells in either static or dynamic (i.e. time lapse) multi-channel images. It enables tracking of two structures (for example SPBs) in two different image channels. For 2D or 3D static images, the locations of the structures are identified, and then intensity values are extracted together with several quantitative parameters, such as length, width, cell orientation, background fluorescence and the distance between the structures of interest. Furthermore, two kinds of kymographs of the tracked structures can be established, one representing the migration with respect to their relative position, the other representing their individual trajectories inside the cell. This software package, called "RodCellJ", allowed us to analyze a large number of S. pombe cells to understand the rules that govern SIN protein asymmetry. CONCLUSIONS: "RodCell" is freely available to the community as a package of several ImageJ plugins to simultaneously analyze the behavior of a large number of rod-shaped cells in an extensive manner. The integration of different image-processing techniques in a single package, as well as the development of novel algorithms does not only allow to speed up the analysis with respect to the usage of existing tools, but also accounts for higher accuracy. Its utility was demonstrated on both 2D and 3D static and dynamic images to study the septation initiation network of the yeast Schizosaccharomyces pombe. More generally, it can be used in any kind of biological context where fluorescent-protein labeled structures need to be analyzed in rod-shaped cells. AVAILABILITY: RodCellJ is freely available under http://bigwww.epfl.ch/algorithms.html, (after acceptance of the publication).

Report of Recommendations to Iowa State University of Science and Technology on the Review of Selected General and Application Controls over the University's Accounts Receivable System, April 6th - May 14th 2004

State University Audit Report

Report of Recommendations to the University of Northern Iowa on a Review of Selected General and Application Controls over the Modern Executive Management Financial Information System, June 7, 2004 through July 29, 2004

State University Audit Report

Report of Recommendations to State University of Iowa on the Review of Selected General and Application Controls Over the Purchasing/Accounts Payable System, June 2 to June 27, 2003

State University Audit Report

Report of Recommendations to Iowa State University of Science and Technology on the Review of Selected General and Application Controls over the Tuition System, April 23 to May 23, 2003

State University Audit Report

Report of Recommendations to the Iowa Department of Transportation on a Review of Selected General and Application Controls Over the Contractor Pay System, April 5, 2004 through May 21, 2004

State Agency Audit Report

Report of Recommendations to the State University of Iowa on the Review of Selected General and Application Controls over the University's Human Resources Information System, June 7, 2005-July 29, 2005

Other Audit Reports - Regent Institutions

Report of Recommendations to the Iowa Department of Transportation on Review of Selected General and Application Controls over the Accounts Payable System, July 11, 2005 to August 3, 2005

State Audit Reports

Report of the Recommendations to the Iowa Department of Workforce Development on a Review of Selected General and Application Controls Over the Unemployment Insurance System, May 1, 2006 to May 24, 2006

State Audit Reports

Report of Recommendations to Iowa State University of Science and Technology on the Review of Selected General and Application Controls over the University's Student Financial Aid System, April 24 through May 12, 2006

State University Audit Report

Audit report on a review of selected general and application controls over the University of Northern Iowa’s Modern Executive Management Financial Information System (MEMFIS) human resources and payroll modules for the period May 22, 2006 through June 12, 2006.

Audit report on a review of selected general and application controls over the University of Northern Iowa’s Modern Executive Management Financial Information System (MEMFIS) human resources and payroll modules for the period May 22, 2006 through June 12, 2006.

Report on a review of selected general and application controls over the Iowa Department of Transportation’s Resource Management System for the period May 5, 2006 through August 4, 2006.

Report on a review of selected general and application controls over the Iowa Department of Transportation’s Resource Management System for the period May 5, 2006 through August 4, 2006.

Setting up a Common European Asylum System : Report on the application of existing instruments and proposals for the new system

The study assesses firstly the evaluation process of the first generation of asylum instruments while underlining the possibilities to improve it. It analyses secondly the asylum "acquis" regarding distribution of refugees between Member States, the eligibility for protection, the status of protected persons regarding detention and vulnerability, asylum procedures and the external dimension by formulating short-term recommendations of each area. Its last part is devoted to the long term evolution of the Common European Asylum System regarding the legal context including the accession of the EU to the Geneva Convention, the institutional perspectives including the new European Support Office, the jurisdictional perspective, the substantive perspective, the distributive perspective and the external perspective.

Audit report on the review of selected general and application controls over the State University of Iowa University of Iowa) ProTrav system for the period June 5, 2006 through July 28, 2006

Audit report on the review of selected general and application controls over the State University of Iowa University of Iowa) ProTrav system for the period June 5, 2006 through July 28, 2006

Report on a review of selected general and application controls over the Iowa Public Employees’ Retirement System (IPERS) Benefits Administration System for the period April 23, 2007 through May 16, 2007

Report on a review of selected general and application controls over the Iowa Public Employees’ Retirement System (IPERS) Benefits Administration System for the period April 23, 2007 through May 16, 2007