Image processing

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-	Cell motility is a complex phenomenon, which may be explored in a variety of experimental systems, ranging from in vitro cultured cells, whole embryos or adult animals. The study of the cell motility takes advantage both of morphological investigations of fixed samples, and of functional analysis of live cells using experimental conditions as soon as possible close to physiological ones. Timelapse-microscopy, in combination with fast optical sectioning techniques, allows to observe and analyze the movement in three dimensions of whole live cells, but also of their subcellular components and of specific molecules at subsequent time steps.	+	Cell motility is a complex phenomenon, which may be explored in a variety of experimental systems, ranging from in vitro cultured cells, whole embryos or adult animals. The study of cell motility takes advantage both of morphological analysis of fixed samples, and of functional studies of live cells, using experimental conditions as close as possible to physiological ones. Timelapse-microscopy, in combination with fast optical sectioning techniques, allows to observe and analyze the movement in three dimensions of whole live cells, but also of their subcellular components and of specific molecules at subsequent time steps.
	*[[Cell motility]]		*[[Cell motility]]
-	:By applying video time lapse techniques to the study of live fibroblasts, the role of specific molecules such as oncogenes and components of the extracellular matrix, has been evaluated both in random condtions and in wound healing assay. A statistical analysis tool giving measure about the speed, the direction and the tortuosity of moving elements has been developed to better support these investigation.	+	:By applying video time lapse techniques to the study of live fibroblasts, the role of specific molecules such as oncogenes and components of the extracellular matrix, has been evaluated both in basal conditions and within wound healing assays. This allowed to define the role of single oncogenes such as Ras and Src in affecting cell motility and their interactions with components of the extracellular matrix. A statistical analysis tool was developed to measure the speed, direction and tortuosity of moving cells.
	*[[Storage of experimental data]]		*[[Storage of experimental data]]
-	:The large number of experimental data and images acquired in time, such as the first set of results obtained, required to develop a systematic procedure to storage and manage the great amount of correlated data. A custom cell bank is in use to archive the history of each cell line, starting from its arrive into the laboratory. To store and manage the large amount of digital images produced has been developed a relational databank able to connect to each acquisition the correlated experimental data such as cell line, colture conditions and staining methods.	+	:The large number of experimental data and images deriving from multiple acquisitions at different times and sample levels stimulated the development of a relational databank, able to connect each acquisition to experimental data such as cell line, colture conditions and staining methods. A custom cell bank maintenance system was also developed to archive the history of each cell line, starting from its arrival to the laboratory and keeping track of the various thawing and propagation procedures.
	*[[Image analysis and processing]]		*[[Image analysis and processing]]
-	:The images, obtained by a conventional fluorescence microscope, contain light from the all 3D sample-objects included within the acquisition field. This means an evident blurring of the focal plane by “out –of - focus” fluorescence. A unix tool executing deconvolution, a specific restoration algorithm, on biological images was developed in order to increase the visibility of some cell structures otherwise hidden. Moreover a suitable visualization and some opportune image processes may highlight various aspects of the image data. This consideration led to the development of IPROC a web based image visualization and processing system. Compatible images range from simple two-dimensional frames, to complex multidimensional datasets, typical of microscopic observation of biological samples, such as time series, z-axis sections, channels recorded at different wavelength and optical arrangement with, optionally, different samples and positions. The program include scrolling, rotation and selection mechanisms to make a variable visualization of a multidimensional image. Processing is obtained by integrating a large library of different unix filters installed on the server, while interactivity is provided by the ability to quickly react to user input via small data requests.IPROC will integrate restoration filters and cell motility tools within one global web system.	+	:Image visualization and processing tools may be used to highlight various, otherwise hidden, aspects of the image data. A web based application, IPROC, is being developed to rapidly visualize and process remotely stored images, within an environment similar to that of a typical desktop application. Compatible images range from simple two-dimensional frames, to complex multidimensional datasets, typical of microscopic observation of biological samples, such as time series, z-axis sections, channels recorded at different wavelength and optical arrangement with, optionally, different samples and positions. The program provides tools for scrolling, rotating on multiple axes and a selection mechanisms to allow a variable visualization of a multidimensional image. Processing is obtained by integrating a large library of different unix filters, installed on the server, while interactivity is provided by the ability to quickly react to user input via small data requests. IPROC will integrate restoration filters and cell motility tools within one global web system.
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-	Cell motility is a complex phenomenon, which may be explored in a variety of experimental situations, ranging from in vitro cultured cells to cell migration in whole embryos or in the adult animal. By applying video time lapse techniques to the study of live fibroblasts, the role of specific molecules such as oncogenes and components of the extracellular matrix has been evaluated. The need for applying image processing techniques to the study, stimulated the development of a number of computational tools, including a system for centralized storage of experimental images, and a web based image processing tool. Statistical analysis of cell movement and study of multidimensional images may be performed within these systems.	+

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Current revision

Cell motility is a complex phenomenon, which may be explored in a variety of experimental systems, ranging from in vitro cultured cells, whole embryos or adult animals. The study of cell motility takes advantage both of morphological analysis of fixed samples, and of functional studies of live cells, using experimental conditions as close as possible to physiological ones. Timelapse-microscopy, in combination with fast optical sectioning techniques, allows to observe and analyze the movement in three dimensions of whole live cells, but also of their subcellular components and of specific molecules at subsequent time steps.

• Cell motility

By applying video time lapse techniques to the study of live fibroblasts, the role of specific molecules such as oncogenes and components of the extracellular matrix, has been evaluated both in basal conditions and within wound healing assays. This allowed to define the role of single oncogenes such as Ras and Src in affecting cell motility and their interactions with components of the extracellular matrix. A statistical analysis tool was developed to measure the speed, direction and tortuosity of moving cells.

• Storage of experimental data

The large number of experimental data and images deriving from multiple acquisitions at different times and sample levels stimulated the development of a relational databank, able to connect each acquisition to experimental data such as cell line, colture conditions and staining methods. A custom cell bank maintenance system was also developed to archive the history of each cell line, starting from its arrival to the laboratory and keeping track of the various thawing and propagation procedures.

• Image analysis and processing

Image visualization and processing tools may be used to highlight various, otherwise hidden, aspects of the image data. A web based application, IPROC, is being developed to rapidly visualize and process remotely stored images, within an environment similar to that of a typical desktop application. Compatible images range from simple two-dimensional frames, to complex multidimensional datasets, typical of microscopic observation of biological samples, such as time series, z-axis sections, channels recorded at different wavelength and optical arrangement with, optionally, different samples and positions. The program provides tools for scrolling, rotating on multiple axes and a selection mechanisms to allow a variable visualization of a multidimensional image. Processing is obtained by integrating a large library of different unix filters, installed on the server, while interactivity is provided by the ability to quickly react to user input via small data requests. IPROC will integrate restoration filters and cell motility tools within one global web system.

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Bioinformatics: Research Activity: Eukaryotic CSTs - Bacterial RNAs - Image processing