Astrocyte Analysis Documentation

Image Processing - Final Project Report
Project 3a - Astrocyte Analysis
Team : Bhaskar Reddy Beerala
Hemanth Kumar Mathi
Aneeshbabu Patchala
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.
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
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
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.
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.