Image processing

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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.	+	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.
-	This research line is focused on the study of cell motility investigating morphological and functional aspects, by experimental systems developed to follow cells in conditions like, as soon as possible, to physiological.	+	*[[Image analysis and processing]]
-	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 or drugs, at subsequent time steps.	+	: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.
-	[[Image:ImagesDB.jpg|center|200px|images data bank]]	+	{{template:footer|footername=footer reslines}}
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-	'''Data bank of biological images and correlated data.''' 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 data bank has also a user-friendly web-interface to visualize and update the image data.	+
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-	[[Image:paths.jpg|center|200px|overlay image and paths]]	+
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-	'''Cell motility tools.''' A set of software tools for visualization and statistical evaluation of cellular movements from sequences of subsequent frames acquired manually or from automated video time-lapse microscopy, has been developed. These tools have been adapted and used to the study of sub-cellular structures migration such as endocytosis vesicles movement, within the cytoplasm.	+
-	The first approach contributed to associate to different cell lines specific motion features; but a punctual analysis is required to study sub-cellular elements in order to make visible their different ability to move into the cytoplasm in response to distinct stimuli. The tools execute statistical analysis to measure the speed, the direction and the tortuosity of moving elements. It takes in input a text file containing cartesian coordinates of each object to follow, time after time.	+
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-	[[Image:actin_original.jpg|200px|right]][[Image:actin_deconv.jpg|200px|right]]	+
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-	'''Software to restore digital images.''' Using optical sectioning technique, a stack of 2D images is obtained. However, due to the nature of the optical system and non-optimal experimental conditions, acquired raw data are usually sensitive to some distorsions. Raw data have to be restored in order to carry out biological analysis and enhance the visibility of cellular structure otherwise hidden. The images, obtained by a conventional fluorescence microscope, contain light from the all 3D sample-object. What is actually present in the focal plane may be blurred by “out –of - focus” fluorescence. The reduction of this effect is carried out by a computational deconvolution process. In theory, this process can be applied to any type of microscope images, but it has often been used to improve images from conventional fluorescence microscopes. Deconvolution algorithms attempt to reassign blurred light to its location.	+
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-	[[Image:IPROC.jpg|right|200px|IPROC]]	+
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-	'''IPROC a web-system to visualize and process biological images.''' 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 images, springing from variable combinations of 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.	+

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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