Saad Ullah Akram

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Time-lapse microscopy imaging has advanced rapidly in last few decades and is producing large volume of data in cell and developmental biology. This has increased the importance of automated analyses, which depend heavily on cell segmentation and tracking as these are the initial stages when computing most biologically important cell properties. In this(More)
Robust cell detection plays a key role in the development of reliable methods for automated analysis of microscopy images. It is a challenging problem due to low contrast, variable fluorescence, weak boundaries, conjoined and overlapping cells, causing most cell detection methods to fail in difficult situations. One approach for overcoming these challenges(More)
which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed. Abstract Tissue, organ and organoid cultures provide suitable models for developmental studies, but our understanding of how the organs are assembled at the single cell level still remains unclear. We describe here a novel(More)
Accurate cell segmentation is vital for the development of reliable microscopy image analysis methods. It is a very challenging problem due to low contrast, weak boundaries, and conjoined and overlapping cells; producing many ambiguous regions, which lower the performance of automated segmentation methods. Cell proposals provide an efficient way of(More)
Live cell imaging in 3D platforms is a highly informative approach to visualize cell function and it is becoming more commonly used for understanding cell behavior. Since these experiments typically generate large data sets their analysis manually would be very laborious and error prone. This has led to the necessity of automatic image analysis tools. Cell(More)
The composition of the matrix molecules is important in in vitro cell culture experiments of e.g. human cancer invasion and vessel formation. Currently, the mouse Engelbreth-Holm-Swarm (EHS) sarcoma -derived products, such as Matrigel®, are the most commonly used tumor microenvironment (TME) mimicking matrices for experimental studies. However, since(More)
Microscopy imaging plays a vital role in understanding many biological processes in development and disease. The recent advances in automation of microscopes and development of methods and markers for live cell imaging has led to rapid growth in the amount of image data being captured. To efficiently and reliably extract useful insights from these captured(More)
Tissue, organ and organoid cultures provide suitable models for developmental studies, but our understanding of how the organs are assembled at the single-cell level still remains unclear. We describe here a novel fixed z-direction (FiZD) culture setup that permits high-resolution confocal imaging of organoids and embryonic tissues. In a FiZD culture a(More)
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