A validated active contour method driven by parabolic arc model for detection and segmentation of mitochondria

Tasel, Serdar F.
Mumcuoğlu, Ünal Erkan
Hassanpour, Reza Z.
Perkins, Guy
Recent studies reveal that mitochondria take substantial responsibility in cellular functions that are closely related to aging diseases caused by degeneration of neurons. These studies emphasize that the membrane and crista morphology of a mitochondrion should receive attention in order to investigate the link between mitochondria] function and its physical structure. Electron microscope tomography (EMT) allows analysis of the inner structures of mitochondria by providing highly detailed visual data from large volumes. Computerized segmentation of mitochondria with minimum manual effort is essential to accelerate the study of mitochondrial structure/function relationships. In this work, we improved and extended our previous attempts to detect and segment mitochondria from transmission electron microcopy (TEM) images. A parabolic arc model was utilized to extract membrane structures. Then, curve energy based active contours were employed to obtain roughly outlined candidate mitochondrial regions. Finally, a validation process was applied to obtain the final segmentation data. 3D extension of the algorithm is also presented in this paper. Our method achieved an average F-score performance of 0.84. Average Dice Similarity Coefficient and boundary error were measured as 0.87 and 14 nm respectively.


Automatic detection of mitochondria from electron microscope tomography images: a curve fitting approach
Tasel, Serdar F.; HASSANPOUR, REZA; Mumcuoğlu, Ünal Erkan; Perkins, Guy; Martone, Maryann (2014-02-18)
Mitochondria are sub-cellular components which are mainly responsible for synthesis of adenosine tri-phosphate (ATP) and involved in the regulation of several cellular activities such as apoptosis. The relation between some common diseases of aging and morphological structure of mitochondria is gaining strength by an increasing number of studies. Electron microscope tomography (EMT) provides high-resolution images of the 3D structure and internal arrangement of mitochondria. Studies that aim to reveal the c...
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...
Computerized detection and segmentation of mitochondria on electron microscope images
Mumcuoğlu, Ünal Erkan; Tasel, S. F.; Perkins, Guy; Martone, M. E.; Gurcan, M. N. (2012-06-01)
Mitochondrial function plays an important role in the regulation of cellular life and death, including disease states. Disturbance in mitochondrial function and distribution can be accompanied by significant morphological alterations. Electron microscopy tomography (EMT) is a powerful technique to study the 3D structure of mitochondria, but the automatic detection and segmentation of mitochondria in EMT volumes has been challenging due to the presence of subcellular structures and imaging artifacts. Therefo...
A high throughput approach for analysis of cell nuclear deformability at single cell level
Ermis, Menekse; Akkaynak, Derya; Chen, Pu; Demirci, Utkan; Hasırcı, Vasıf Nejat (2016-11-14)
Various physiological and pathological processes, such as cell differentiation, migration, attachment, and metastasis are highly dependent on nuclear elasticity. Nuclear morphology directly reflects the elasticity of the nucleus. We propose that quantification of changes in nuclear morphology on surfaces with defined topography will enable us to assess nuclear elasticity and deformability. Here, we used soft lithography techniques to produce 3 dimensional (3-D) cell culture substrates decorated with micron ...
Automatic segmentation of mitochondria in scanning electron microscopy images
Güven, Mehmet Çağrı; Mumcuoğlu, Ünal Erkan; Department of Information Systems (2021-9-7)
Many studies have shown that shape of mitochondria indicates the occurrence of diseases. Scanning Electron Microscopy (SEM) enables to obtain image of internal structures of the cell and mitochondria. Automatic segmentation of mitochondria contributes to the decision of diseases by specialists. There is limited study about automatic segmentation of mitochondria in Serial Block-Face Scanning Electron Microscopy (SFBSEM) images. SBFSEM imaging technique provides full automation, well registered images, less t...
Citation Formats
S. F. Tasel, Ü. E. Mumcuoğlu, R. Z. Hassanpour, and G. Perkins, “A validated active contour method driven by parabolic arc model for detection and segmentation of mitochondria,” JOURNAL OF STRUCTURAL BIOLOGY, pp. 253–271, 2016, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/32407.