Semi-automatic segmentation of mitochondria on electron microscopy images using kalman filtering approach

Download

index.pdf

Date

2016

Author

Mohammadi Alamdari, Aynaz

Metadata

Show full item record

Item Usage Stats

194
views

86
downloads

Mitochondria are membrane bound organelles found in most eukaryotic cells. Mitochondria provide cell’s energy; hence they are called ‘power houses of the cell’. The structure of mitochondria can be illustrated in an electron micrograph. This structure has two membranes: inner and outer. There is a gap between these two membranes, called inter-membrane space. Folds of inner membrane inside the mitochondria form the cristae. To study the relation between mitochondria’s physical structure and its function, electron microscope tomography (EMT) is used to visualize mitochondria. EMT provides 3D structure of mitochondria in high resolution images. In the slices of tomographic images provided by EMT, mitochondria appear as elliptical structures. The cristae are also visualized in these images with various pathology and biological variations. One of the preferred method can be semi-automatic segmentation; since manual segmentation in medical images is time and energy consuming and tedious; moreover fully automatic methods also fail in medical images and cause incorrect results because of low quality of images and restrictions imposed by image acquisition. In this work, an endeavour is made to segment mitochondrial outer boundary using active contour, Kalman filter and optical flow. In the first slice of the images, a contour is provided by user. Then, for the other slices, position values and velocity values calculated using the active contour and optical flow (respectively) are combined with the Kalman filter to predict the points of the boundary in the next slice. In addition, a set of automatic and semi-automatic tools are developed to determine splitting and merging mitochondria, and to segment them.

Subject Keywords

Mitochondria., Kalman filtering., Electron microscopy., Imaging systems in medicine.

URI

http://etd.lib.metu.edu.tr/upload/12619922/index.pdf
https://hdl.handle.net/11511/25601

Collections

Graduate School of Informatics, Thesis

Suggestions

OpenMETU
Core

Semi-automatic segmentation of mitochondria on transmission electron microscopy images using live-wire and surface dragging methods Farzin Asanjan, Mahdieh; Mumcuoğlu, Ünal Erkan; Hassanpour, Reza Zare; Department of Medical Informatics (2017) Mitochondria are cytoplasmic organelles of the cell, which have significant role in the variety of cellular metabolic functions. Mitochondria act as the power plants of the cell, and are surrounded by two membranes. Significant morphological alterations are often due to changes in mitochondrial functions. A powerful technique in order to study the three-dimensional (3D) structure of mitochondria and its alterations in disease states is Electron microscope tomography. Due to the presence of various subcellul...
Semi-automatic/user-guided segmentation of mitochondria on transmission electron microscopy images Çöçelli, Mustafa; Mumcuoğlu, Ünal Erkan; Hassanpour, Reza; Department of Medical Informatics (2015) The purpose of the study is to develop and implement some user-guided/semi-automatic methods to segment mitochondria on transmission electron microscopy images. Earlier automatic active contour based detection and segmentation algorithm applied on slices of mitochondria dataset are subject to some errors. Therefore, semi-automatic methods are necessary to adjust structure of wrongly detected and segmented mitochondria. There are six semi-automatic methods introduced in this thesis, namely, splitting, mergin...
Detection and segmentation of mitochondria from electron microscope tomography images Taşel, Faris Serdar; Mumcuoğlu, Ünal Erkan; Hassanpour, Reza Zare; Department of Medical Informatics (2016) Recent studies exhibit that mitochondria have a significant role in cellular functions that are associated to the diseases of aging caused by neuron degeneration. These studies accentuate that the peripheral membrane and crista morphology of a mitochondrion deserves attention in order to reveal the relation between mitochondrial function and its physical structure. The analysis of the inner structures of mitochondria is carried out by electron microscope tomography (EMT) which provides detailed visualizatio...
Crossflow ultrafiltration of Bacillus licheniformis fermentation medium to separate protease enzymes Takac, S; Elmas, S; Çalık, Pınar; Ozdamar, TH (2001-01-01) Separation conditions for the serine alkali protease (SAP) enzyme from the neutral protease and amylase enzymes of Bacillus licheniformis cells were investigated in a crossflow ultrafiltration system by using 30 000 Da MWCO polysulphone membrane. The effects of initial enzyme concentration and recirculation velocity on the permeate flux, on the total resistance, and on the recovery yield of SAP in the permeate were investigated. High permeate flux was obtained at high recirculation velocity but at low initi...
Effect of cortex stiffness variation on cleavage in animal cells AKKAS, N; KERMANIAN, M (1993-09-29) Cytokinesis is the division of the cytoplasm and the plasma membrane into two. Nuclear division and cytokinesis take a relatively short time to happen in animal cells in which cytokinesis takes place by means of furrowing. Here we consider the cleavage of the animal cells only. Although the basic division mechanisms appear to be similar in all animal cells, the divisions that take place during early embryonic development, which are termed as cleavages, are not exactly the same as those that occur later. In ...

Citation Formats

A. Mohammadi Alamdari, “Semi-automatic segmentation of mitochondria on electron microscopy images using kalman filtering approach,” M.S. - Master of Science, Middle East Technical University, 2016.