• Title/Summary/Keyword: Confocal microscopy

Search Result 436, Processing Time 0.035 seconds

Automated 3D scoring of fluorescence in situ hybridization (FISH) using a confocal whole slide imaging scanner

  • Ziv Frankenstein;Naohiro Uraoka;Umut Aypar;Ruth Aryeequaye;Mamta Rao;Meera Hameed;Yanming Zhang;Yukako Yagi
    • Applied Microscopy
    • /
    • v.51
    • /
    • pp.4.1-4.12
    • /
    • 2021
  • Fluorescence in situ hybridization (FISH) is a technique to visualize specific DNA/RNA sequences within the cell nuclei and provide the presence, location and structural integrity of genes on chromosomes. A confocal Whole Slide Imaging (WSI) scanner technology has superior depth resolution compared to wide-field fluorescence imaging. Confocal WSI has the ability to perform serial optical sections with specimen imaging, which is critical for 3D tissue reconstruction for volumetric spatial analysis. The standard clinical manual scoring for FISH is labor-intensive, time-consuming and subjective. Application of multi-gene FISH analysis alongside 3D imaging, significantly increase the level of complexity required for an accurate 3D analysis. Therefore, the purpose of this study is to establish automated 3D FISH scoring for z-stack images from confocal WSI scanner. The algorithm and the application we developed, SHIMARIS PAFQ, successfully employs 3D calculations for clear individual cell nuclei segmentation, gene signals detection and distribution of break-apart probes signal patterns, including standard break-apart, and variant patterns due to truncation, and deletion, etc. The analysis was accurate and precise when compared with ground truth clinical manual counting and scoring reported in ten lymphoma and solid tumors cases. The algorithm and the application we developed, SHIMARIS PAFQ, is objective and more efficient than the conventional procedure. It enables the automated counting of more nuclei, precisely detecting additional abnormal signal variations in nuclei patterns and analyzes gigabyte multi-layer stacking imaging data of tissue samples from patients. Currently, we are developing a deep learning algorithm for automated tumor area detection to be integrated with SHIMARIS PAFQ.

Investigation of the Antifungal Activity and Mechanism of Action of LMWS-Chitosan

  • Park, Yoon-Kyung;Kim, Mi-Hyun;Park, Seong-Cheol;Cheong, Hyeon-Sook;Jang, Mi-Kyeong;Nah, Jae-Woon;Hahm, Kyung-Soo
    • Journal of Microbiology and Biotechnology
    • /
    • v.18 no.10
    • /
    • pp.1729-1734
    • /
    • 2008
  • Chitosan, a cationic polysaccharide, has been widely used as a dietary supplement and in a variety of pharmacological and biomedical applications. The antifungal activity and mechanism of action of low molecular weight water-soluble chitosan (LMWS-chitosan) were studied in fungal cells and vesicles containing various compositions of fungal lipids. LMWS-chitosan showed strong antifungal activity against various pathogenic yeasts and hyphae-forming fungi but no hemolytic activity or cytotoxicity against mammalian cells. The degree of calcein leakage was assessed on the basis of lipid composition (PC/CH; 10:1, w/w). Our result showing that LMWS-chitosan interacts with liposomes demonstrated that chitosan induces leakage from zwitterionic lipid vesicles. Confocal microscopy revealed that LMWS-chitosan was located in the plasma membrane. Finally, scanning electron microscopy revealed that LMWS-chitosan causes significant morphological changes on fungal surfaces. Its potent antibiotic activity suggests that LMWS-chitosan is an excellent candidate as a lead compound for the development of novel anti-infective agents.

Segmentation of Neuronal Axons in Brainbow Images

  • Kim, Tae-Yun;Kang, Mi-Sun;Kim, Myoung-Hee;Choi, Heung-Kook
    • Journal of Korea Multimedia Society
    • /
    • v.15 no.12
    • /
    • pp.1417-1429
    • /
    • 2012
  • In neuroscientific research, image segmentation is one of the most important processes. The morphology of axons plays an important role for researchers seeking to understand axonal functions and connectivity. In this study, we evaluated the level set segmentation method for neuronal axons in a Brainbow confocal microscopy image. We first obtained a reconstructed image on an x-z plane. Then, for preprocessing, we also applied two methods: anisotropic diffusion filtering and bilateral filtering. Finally, we performed image segmentation using the level set method with three different approaches. The accuracy of segmentation for each case was evaluated in diverse ways. In our experiment, the combination of bilateral filtering with the level set method provided the best result. Consequently, we confirmed reasonable results with our approach; we believe that our method has great potential if successfully combined with other research findings.

Confocal laser scanning microscopy image를 이용한 UASB granule의 메탄 생성 능력 측정

  • Lee, Yu-Jin;Kim, Hyo-Seop;An, Yeong-Hui;Park, Seong-Hun
    • 한국생물공학회:학술대회논문집
    • /
    • 2000.04a
    • /
    • pp.365-369
    • /
    • 2000
  • Methanogenic activity of granular sludge was monitored by specific methanogenic activity (SMA) assay and confocal laser scanning microscopy (CLSM) during start-up of a thermophilic UASB reactor. Autofluorescence by CLSM could visualize the methanogenic bacterial population inside sludge granules and its intensity was proportional to SMA. Considering the complex procedures of SMA measurement, fluorescence quantification by CLSM can be suggested as a routine technique measuring methanogenic activity in UASB granules.

  • PDF

Flexure hinge mechanism having amplified rectilinear motion for confocal scanning microscopy using optical section

  • Kwon, Oh-Kyu;Park, Poo-Gyeon
    • 제어로봇시스템학회:학술대회논문집
    • /
    • 2001.10a
    • /
    • pp.162.6-162
    • /
    • 2001
  • Confocal scanning microscopy (CSM) is an important instrument in a wide variety of imaging applications because of its ability to provide three-dimensional images of thick, volume specimens. The mechanism for two-dimensional beam scanning and optical sectioning has an important roe in CSM as the three-dimensional profiler. This optical sectioning property arises from the use of a point detector, which serves to attenuate the signals from out-of-focus. The intensity profile for the open loop scanning should be matched with its response for the standard. The non-linearity can be minimized with the optical sectioning or the optical probe of the closed loop control. This paper shows the mathematical expression of the light such as the extinction curve in the optical fields of system using AO deflector, the axial/lateral response experimentally when the error sources change, and the methods of optical sectioning. Thorough design of optical sectioner is crucial to the success of CSM in the field ...

  • PDF

Indented Surface Configuration and its Volume Calculation (압입 표면형상의 구현과 체적계산법)

  • Yang, Jae-Yong;Yoon, Moon-Chul
    • Journal of the Korean Society of Manufacturing Technology Engineers
    • /
    • v.21 no.5
    • /
    • pp.708-713
    • /
    • 2012
  • The indented geometry for rockwell hardness indenter has been configured by using Confocal Laser Scanning Microscopy (CLSM). For this purpose, the CLSM can be well suited to construct the three-dimensional indented volume from the indented surface by rockwell hardness tester. Furthermore, the height data of HEI(height encoded image) by CLSM must be acquired at first and converted to indented surface later. And the indented surface patterns enable us to predict the indenter shape and volume. This volume can be used to study the rockwell hardness model as a volume parameter. As a result, the technique performed in this study by combining the CLSM with compensation technique is an excellent one to obtain the geometries of indented surfaces over a wide range of surface resolution in a micro scale. And it can be used for micro volume calculation.

Potassium Distribution in the Apical Region of Rice Root

  • Rehman Shafiq;Park Moung-Ryoul;Ashraf Muhammad;Yun Song-Joong
    • KOREAN JOURNAL OF CROP SCIENCE
    • /
    • v.51 no.4
    • /
    • pp.295-297
    • /
    • 2006
  • Potassium (K) distribution in rice (Oryza sativa L.) root was studied by confocal laser microscopy, using potassium sensitive fluorescent dye potassium-binding benzofuran isophthalate (PBFI). Significantly high intensity of K-specific fluorescence was detected at the root cap region followed by meristematic and basal regions. A negligible or fainted fluorescence was observed at the root hairs area. These results suggest that K is heavily distributed in the apical area of rice root, which may be required in higher concentration for division and extension of cells, as it is the rapidly growing region of the root, moreover, may also be involved in water uptake by creating osmotic gradient across membranes.

Development of confocal scanning microscopy using acousto-optica1 deflector

  • J.W. Seo;D.K. Kang;H.G. Yun;Kim, K.H.;D.G. Gweon
    • 제어로봇시스템학회:학술대회논문집
    • /
    • 2001.10a
    • /
    • pp.161.6-161
    • /
    • 2001
  • Confocal scanning microscopy (CSM) has an important role as the three-dimensional profiler. An image distribution can be reconstructed by a correlation analysis of spots with the bandwidth of radio frequency. But it is a serious problem for the high performance to align the optical components. Especially, the parasitic motion of focus on the detector gives rise to the fatal distortion of an image profile named the extinction effect while using acousto-optical(AO) deflector. An image profile can be regenerated in CSM with many advantages of non-contact, high speed and high resolution comparatively. In addition to the axial response of the primary focus, the lateral movement of it gives a necessity of the unitary lens to the scanning system. While using the beam deflector, the pupil of beam may be fixed at the nominal position. Furthermore, the use of a deflector may result in ...

  • PDF

Light microscopic evidence of in vivo differentiation from the transplanted inferior turbinate-derived stem cell into the rod photoreceptor in degenerating retina of the mouse

  • Yong Soo Park;Yeonji Kim;Sung Won Kim; In-Beom Kim
    • Applied Microscopy
    • /
    • v.50
    • /
    • pp.11.1-11.3
    • /
    • 2020
  • The human turbinate-derived mesenchymal stem cells (hTMSCs), which were DiI-labeled and transplanted into the subretinal space in degenerating mouse retina, were observed in retinal vertical sections processed for rhodopsin (a marker for rod photoreceptor) by confocal microscope with differential interference contrast (DIC) filters. The images clearly demonstrated that DiI-labeled hTMSCs have rhodopsin-immunoreactive appendages, indicating differentiation of transplanted hTMSC into rod photoreceptor. Conclusively, the finding suggests therapeutic potential of hTMSCs in retinal degeneration.