Object-Oriented Segmentation of Cell Nuclei in Fluorescence Microscopy Images

Koyuncu, Can Fahrettin
Atalay, Rengül
Cell nucleus segmentation remains an open and challenging problem especially to segment nuclei in cell clumps. Splitting a cell clump would be straightforward if the gradients of boundary pixels in-between the nuclei were always higher than the others. However, imperfections may exist: inhomogeneities of pixel intensities in a nucleus may cause to define spurious boundaries whereas insufficient pixel intensity differences at the border of overlapping nuclei may cause to miss some true boundary pixels. In contrast, these imperfections are typically observed at the pixel-level, causing local changes in pixel values without changing the semantics on a large scale. In response to these issues, this article introduces a new nucleus segmentation method that relies on using gradient information not at the pixel level but at the object level. To this end, it proposes to decompose an image into smaller homogeneous subregions, define edge-objects at four different orientations to encode the gradient information at the object level, and devise a merging algorithm, in which the edge-objects vote for subregion pairs along their orientations and the pairs are iteratively merged if they get sufficient votes from multiple orientations. Our experiments on fluorescence microscopy images reveal that this high-level representation and the design of a merging algorithm using edge-objects (gradients at the object level) improve the segmentation results. (c) 2018 International Society for Advancement of Cytometry


Iterative H-Minima-Based Marker-Controlled Watershed for Cell Nucleus Segmentation
Koyuncu, Can Fahrettin; Akhan, Ece; Erşahin, Tülin; Atalay, Rengül; GÜNDÜZ DEMİR, Çiğdem (Wiley, 2016-04-01)
Automated microscopy imaging systems facilitate high-throughput screening in molecular cellular biology research. The first step of these systems is cell nucleus segmentation, which has a great impact on the success of the overall system. The marker-controlled watershed is a technique commonly used by the previous studies for nucleus segmentation. These studies define their markers finding regional minima on the intensity/gradient and/or distance transform maps. They typically use the h-minima transform bef...
Structural properties of an engineered outer membrane protein G mutant, OmpG-16SL, investigated with infrared spectroscopy
Yilmaz, Irem; Yildiz, Ozkan; KORKMAZ ÖZKAN, FİLİZ (Informa UK Limited, 2019-05-31)
The structural and functional differences between wild type (WT) outer membrane protein G and its two mutants are investigated with Fourier transform infrared spectroscopy. Both mutants have a long extension to the primary sequence to increase the number of beta-strands from 14 (wild type) to 16 in an attempt to enlarge the pore diameter. The comparison among proteins is made in terms of pH-dependent conformational changes and thermal stability. Results show that all proteins respond to pH change but at dif...
DynaDom: structure-based prediction of T cell receptor inter-domain and T cell receptor-peptide-MHC (class I) association angles
Hoffmann, Thomas; Marıon, Antoıne; Antes, Iris (Springer Science and Business Media LLC, 2017-02-02)
Background: T cell receptor (TCR) molecules are involved in the adaptive immune response as they distinguish between self- and foreign-peptides, presented in major histocompatibility complex molecules (pMHC). Former studies showed that the association angles of the TCR variable domains (Va/V beta) can differ significantly and change upon binding to the pMHC complex. These changes can be described as a rotation of the domains around a general Center of Rotation, characterized by the interaction of two highly...
Neurosecretory cells in the molluses Helix have perikarya that show clear signs of adaptation for both the synthesis and the discharge of secretory material. They are characterized morphologically by juxtaposition with the neural lamella. Passage of hormone into the haemocoel is apparently facilitated in many cases by the extreme attenuation of areas of the lamella and perineurium adjacent to the perikarya and by other forms of histological differentiation. Presumptive sites of release are characterized by ...
The expression of GST isoenzymes and p53 in non-small cell lung cancer.
Oguztßzun, Serpil; Aydin, Mehtap; Demirag, Funda; Yazici, Ulkß; Ozhavzali, Mßzeyyen; Kiliç, Murat; Can, Mesude IŠ(VM Media SP. zo.o VM Group SK, 2010-6-10)
This study investigated the immunohistochemical staining characteristics of glutathione-S-transferase alpha, pi, mu, theta and p53 in non-small cell lung carcinoma and normal lung tissue from 50 patients. The relationships between expressions of the Glutathione-S-transferase isoenzymes and some clinicopathological features were also examined. Expression of glutathione-S-transferase pi, mu, alpha, theta and p53 was assessed by immunohistochemistry for primary lung carcinomas of 50 patients from the Sanitariu...
Citation Formats
C. F. Koyuncu, R. Atalay, and Ç. GÜNDÜZ DEMİR, “Object-Oriented Segmentation of Cell Nuclei in Fluorescence Microscopy Images,” CYTOMETRY PART A, pp. 1019–1028, 2018, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/62776.