Image Processing - Final Project Report Project 3a - Astrocyte Analysis Team : Bhaskar Reddy Beerala Hemanth Kumar Mathi Aneeshbabu Patchala Abstract: The importance of astrocyte-neuron communication in neuronal development and synaptic plasticity has become increasingly clear. In fact, recent studies indicate that astrocytes are morphologically and functionally diverse and play critical roles in neurodevelopmental diseases such as Rett syndrome and fragile X mental retardation. In this report, we are saying that we have developed a plugin that separates astrocytes(glial cells) from neurons. We are performing segmentation for the task to be done. It has been discovered in recent years that astrocytes not only function as gap fillers and structural supports, but play an active role in supporting the normal functions of neurons, oligodendrocytes, neural stem cells, blood-brain barrier, and so on. They regulate the extracellular ionic and chemical environment, respond to CNS injury, and play a fundamental role in the pathogenesis of ischemic neuronal death, and they have remained as one of the most active research areas in neuroscience. Glial cells represent the largest cell population in the central nervous system (CNS). They are divided into three categories: astrocytes, the most abundant glial cell type, oligodendrocytes, the central equivalent of Schwann cells, and microglial cells, which share features with immune cells. For decades, astrocytes were essentially considered to be passive elements providing a structural support for neurons and contributing to the blood-brain barrier by wrapping processes around CNS microvessels. Several physiological properties related to CNS homeostasis (clearance and metabolism of neurotransmitters, regulation of extracellular pH, and K+ level) have also been attributed to astrocytes, which thereby contribute to the maintenance of an ideal environment for neuronal cell function. Introduction: Until relatively recently, astrocytes, along with other cells of the glial lineage such as oligodendrocytes and microglia, were believed to be structural cells, the main function of which was to hold neurons together. It is now known, however, that astrocytes serve many housekeeping functions, including maintenance of the extracellular environment and stabilization of cell–cell communications in the CNS. The function of astrocytes in regulating cerebral blood flow and maintaining synaptic function is becoming increasingly recognized as being of paramount importance in the maintenance of the neuronal environment. Astrocytes are also central to the maintenance of neuronal metabolism and neurotransmitter synthesis. Understanding these functions has allowed a refocusing with regard to the role of astrocytes in neurodegenerative diseases, which has led to astrocyte-specific analyses with potential for drug discovery. Astrocytes also known collectively as astroglia, are characteristic star-shaped glial cells in the brain and spinal cord. They are the most abundant cell of the human brain. They perform many functions, including biochemical support of endothelial cells that form the blood–brain barrier, provision of nutrients to the nervous tissue, maintenance of extracellular ion balance, and a role in the repair and scarring process of the brain and spinal cord following traumatic injuries. For identifying these astrocytes we were given some tiff extended images, where we can find these astrocytes. For the process of segmentation, we need to apply threshold to the image, prior to that image should be converted to 8-bit. Threshold should be applied and adjusted such that these astrocytes can be identified without noise. If we observe any cells joining each other, at that point of time we need to apply watershed to those cells, such that they can be separated with border. After observing that these glial cells are separated without any kind of noise, we can proceed with the segmentation process in 3D. Whenever the segmentation is done, we need to analyze the cells in terms of Volume, surface area etc., Technology and Tools used for the implementation: Used Java as Code behind Used ImageJ tool for the implementation Implementation and Results: Astrocytes are characteristic star-shaped glial cells in the brain and spinal cord. We need to clearly segment those star-shaped cells. So that we can easily count the number of cells in the body by this segmenting. We can understand the functionality of each cell very clearly. After segmenting these glial cells in 3D, certain parameters are analyzed like surface area, volume . As I have already mentioned that, we are using ImageJ tool for this development, after loading the image it needs to be converted to 8-bit. Then we need to apply threshold, until the noise in the image is removed. At the same time we are slicing the images count. While slicing the images we are considering the images where we observe astrocytes, by removing all other images. Next after thresholding, seed points are placed to identify the glial cells by using ROI Manager so that segmentation can be done easily. When ever these seed points are placed, we are applying level sets segmentation, so that these glial cells can be highlighted very clearly. From the above figures, we can observe the green structure, we have placed seed points on the glial cell, based on that point the structure is enlarged and this is formed. Here is the final segment, where we can observe two glial cells in different images. After the segmentation process is done, we need to analyze particles in certain aspects like count of the glial cells, surface area of cells, Volume of cells etc., We have two glial cells found, so we can observe the count as "2" in the above figure. Now those segmented cells must be show in 3D viewer. Conclusion: Hence, we segmented the glail cells in a considered image and analyzed the particles such as count of the glial cells, volume, surface area, no of voxels present in it etc.., Finally the segmented image is viewed in 3D for better understanding. References: http://www.jbc.org/content/278/27/24438.long http://www.nature.com/nrneurol/journal/v2/n12/full/ncpneuro0355.html http://imagej.nih.gov/ij/developer/api/ http://rsb.info.nih.gov/ij/plugins/