Computerized detection and segmentation of mitochondria on electron microscope images

2012-06-01
Mumcuoğlu, Ünal Erkan
Tasel, S. F.
Perkins, Guy
Martone, M. E.
Gurcan, M. N.
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. Therefore, the interpretation, measurement and analysis of mitochondrial distribution and features have been time consuming, and development of specialized software tools is very important for high-throughput analyses needed to expedite the myriad studies on cellular events. Typically, mitochondrial EMT volumes are segmented manually using special software tools. Automatic contour extraction on large images with multiple mitochondria and many other subcellular structures is still an unaddressed problem. The purpose of this work is to develop computer algorithms to detect and segment both fully and partially seen mitochondria on electron microscopy images. The detection method relies on mitochondria's approximately elliptical shape and double membrane boundary. Initial detection results are first refined using active contours. Then, our seed point selection method automatically selects reliable seed points along the contour, and segmentation is finalized by automatically incorporating a live-wire graph search algorithm between these seed points. In our evaluations on four images containing multiple mitochondria, 52 ellipses are detected among which 42 are true and 10 are false detections. After false ellipses are eliminated manually, 14 out of 15 fully seen mitochondria and 4 out of 7 partially seen mitochondria are successfully detected. When compared with the segmentation of a trained reader, 91% Dice similarity coefficient was achieved with an average 4.9 nm boundary error.
JOURNAL OF MICROSCOPY

Suggestions

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...
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...
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 (2016-06-01)
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 l...
Numerical modeling and experimental investigation of cell manipulation using acoustophoresis
Karaman, Alara; Özer, Mehmet Bülent; Department of Mechanical Engineering (2022-8-24)
Several diseases, such as sickle cell disease and cancer, can affect the properties of cells. Manipulation or separation of the altered cell is necessary to diagnose such diseases. Acoustophoresis, the migration of particles by using acoustic standing waves, is a promising technique for bio-particle manipulation. This thesis presents numerical modelling and experimental investigation of using acoustophoresis for cell manipulation purposes. First, the trajectories of the cells in an acoustophoretic chip are ...
Development of sandwich type nucleic acid array platform for the detection of micrornas in breast cancer
Atılgan, Seren; Öktem, Hüseyin Avni; Department of Biology (2014)
MicroRNAs are small non-coding RNAs that are involved in important regulatory pathways such as differentiation, development, metabolism, cell proliferation, and cell death. Several recent research show that deregulated expression of miRNAs has crucial roles in disease pathologies, mainly in cancer. Therefore, it is likely that the usage of miRNAs as diagnostic and prognostic biomarkers in patients and the development of various techniques for the detection of microRNA in clinical research will become widesp...
Citation Formats
Ü. E. Mumcuoğlu, S. F. Tasel, G. Perkins, M. E. Martone, and M. N. Gurcan, “Computerized detection and segmentation of mitochondria on electron microscope images,” JOURNAL OF MICROSCOPY, pp. 248–265, 2012, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/32292.