Extracting Cell and Fibre Orientation from Microscopic Images:Computational Methods and Tools

Abstract

Orientation of cell and its actin fibres dictate various properties of the cell and its associated tissue including morphology, cell migration and response of cell to external stimuli. While the vital role of cell and actin fibre orientation has been demonstrated in various studies and across many cell-types, extracting this information from microscopy images is a challenging task. Although several methods have been developed to quantify alignment of a cell and its actin fibres from experimental images, all of them differ at one step or the other. We highlight the importance of orientation of cell and associated fibres and present a generic scheme of various approaches to assimilate the widely used methods. We have presented a systematic approach to determine cell and fibre orientation. The study will improve our understanding of the core processes and will also help in development of high throughput imaging methods to extract information from experimental images.Keywords: BEAS, cell orientation, DFT, fibre orientation, FFT, image processing, thresholding.IN the study of biological phenomena, cell is at a very fundamental level, as it is the smallest building block of all organisms. In fact, it is the smallest form of life that exhibits all the basic traits that form life such as birth, ingestion, digestion, protection and finally death. Cell during its life cycle experiences a number of mechanical interactions with surrounding environment necessary for its communication, proliferation, differentiation and migration [1][2][3][4][5][6][7][8] . A cell responds to these mechanical forces by exhibiting changes at various levels such as in morphology, protein synthesis 9,10 , gene expression 11,12 , etc. Then, cell tries to adapt to its environment through these changes. Several of its mechanical properties facilitate the adaptation of cell to the associated environment. Therefore, to understand the mechanism of working of a cell, knowledge of its mechanical properties and how do these get affected by a cell's surrounding environment is very vital. Microscopy-based imaging and its subsequent analysis is one of the traditional and widely used approaches to gain insights into the cell's mechanical and morphological properties. While microscopy imaging is a widely used approach to extract quantitative information about cell morphology, image analysis and morphology quantification are still challenging. One of the morphological features of a cell, which has been shown to exhibit several genotypic and phenotypic properties of a cell is the orientation of the cell. Similarly, orientation of fibres has been shown to exhibit various properties of associated cell population, including their density, topography, etc.The orientation of cell and the associated fibres are the indicative of many physiological and disease conditions. While microscopy-based image acquisition is the traditional method to gain insights into the orientation and morphology of cell and associated fibres, extracting thequantitative information about the c...

Substrate-dependent control of the chiral orientation of mesenchymal stem cells: image-based quantitative profiling

“…The region-based active-contour method is advantageous, as this type of method is less sensitive to image noise and robust against initial curve placement [19]. However, in low-contrast images, the activecontour method is sensitive to the initial position, which can result in inaccurate cell segmentation [20]. Moreover, this method cannot effectively segment contiguous cells.…”

“…The frequency components (horizontal and vertical) obtained from this analysis were included in the Fourier domain. The frequency components were further converted into polar coordinates to obtain magnitudes and angular values (α) [19,20].…”