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For potential applications in bioscience, a two-fingered microhand with dexterous manipulation capability was developed. This microhand system could perform dexterous tasks such as cell rotation, single cell pick-and-place, cell patterning, and measurement of mechanical properties of living cells. However, it is a tedious task to manipulate micro objects manually. In order to improve the efficiency...
Network structures formed by actin filaments are present in many kinds of fluorescence microscopy images. In order to quantify the conformations and dynamics of such actin filaments, we propose a fully automated method to extract actin networks from images and analyze network topology. The method handles well intersecting filaments and, to some extent, overlapping filaments. First we automatically...
While basic principles of microtubule organization are well understood, much remains to be learned about the extent and significance of variation in that organization among cell types and conditions. Large numbers of images of microtubule distributions for many cell types can be readily obtained by high throughput fluorescence microscopy but direct estimation of the parameters underlying the organization...
We present a cell cycle analysis that aims towards improving our previous work by adding another channel and using one more dimension. The data we use is a set of 3D images of mouse cells captured with a spinning disk confocal microscope. All images are available in two channels showing the chromocenters and the fluorescently marked protein PCNA, respectively. In the present paper, we will describe...
The local three-dimensional (3D) microenvironment of a cell is known to affect it during various processes such as tissue morphogenesis, wound healing and cancer progression. However, the structural properties of the 3D microenvironment's extracellular matrix (ECM) does not usually change after the initial properties are set. This paper presents a method to dynamically and reversibly modify 3D ECM...
In this paper, we apply iterative transform algorithms, namely the error reduction algorithm and the hybrid input-output algorithm, to retrieve missing data in 3D reconstruction from 2D crystal images. 3D protein structures are determined using cryo-electron microscopy (cryo-EM). Extremely strong noise in cryo-EM brings in unreliable artifacts and a limited number of projections leave missing components...
This paper describes free software (called Acquiarium, http://cbia.fi.muni.cz/acquiarium.html) for carrying out the common pipeline of many spatial cell studies using fluorescence microscopy. It addresses image capture, raw image correction, image segmentation, the quantification and spatial arrangement of segmented objects, volume rendering, and statistical evaluation. The software is designed for...
Biological shape modeling is an essential task that is required for systems biology efforts to simulate complex cell behaviors. Statistical learning methods have been used to build generative shape models based on reconstructive shape parameters extracted from microscope image collections. However, such parametric modeling approaches are usually limited to simple shapes and easily-modeled parameter...
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