The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform

Christine L Clarke - One of the best experts on this subject based on the ideXlab platform.

  • open source tools for management and archiving of Digital Microscopy data to allow integration with patient pathology and treatment information
    arXiv: Image and Video Processing, 2020
    Co-Authors: Matloob Khushi, Georgina Edwards, Diego Marcos, Jane E Carpenter, Dinny J Graham, Christine L Clarke
    Abstract:

    Virtual Microscopy includes digitisation of histology slides and the use of computer technologies for complex investigation of diseases such as cancer. However, automated image analysis, or website publishing of such Digital images, is hampered by their large file sizes. We have developed two Java based open source tools: Snapshot Creator and NDPI-Splitter. Snapshot Creator converts a portion of a large Digital slide into a desired quality JPEG image. The image is linked to the patients clinical and treatment information in a customised open source cancer data management software (Caisis) in use at the Australian Breast Cancer Tissue Bank (ABCTB) and then published on the ABCTB website this http URL using Deep Zoom open source technology. Using the ABCTB online search engine, Digital images can be searched by defining various criteria such as cancer type, or biomarkers expressed. NDPI-Splitter splits a large image file into smaller sections of TIFF images so that they can be easily analysed by image analysis software such as Metamorph or Matlab. NDPI-Splitter also has the capacity to filter out empty images. Snapshot Creator and NDPI-Splitter are novel open source Java tools. They convert Digital slides into files of smaller size for further processing. In conjunction with other open source tools such as Deep Zoom and Caisis, this suite of tools is used for the management and archiving of Digital Microscopy images, enabling digitised images to be explored and zoomed online. Our online image repository also has the capacity to be used as a teaching resource. These tools also enable large files to be sectioned for image analysis.

  • open source tools for management and archiving of Digital Microscopy data to allow integration with patient pathology and treatment information
    Diagnostic Pathology, 2013
    Co-Authors: Matloob Khushi, Georgina Edwards, Diego Marcos, Jane E Carpenter, Dinny J Graham, Christine L Clarke
    Abstract:

    Background: Virtual Microscopy includes digitisation of histology slides and the use of computer technologies for complex investigation of diseases such as cancer. However, automated image analysis, or website publishing of such Digital images, is hampered by their large file sizes. Results: We have developed two Java based open source tools: Snapshot Creator and NDPI-Splitter. Snapshot Creator converts a portion of a large Digital slide into a desired quality JPEG image. The image is linked to the patient’s clinical and treatment information in a customised open source cancer data management software (Caisis) in use at the Australian Breast Cancer Tissue Bank (ABCTB) and then published on the ABCTB website (http://www. abctb.org.au) using Deep Zoom open source technology. Using the ABCTB online search engine, Digital images can be searched by defining various criteria such as cancer type, or biomarkers expressed. NDPI-Splitter splits a large image file into smaller sections of TIFF images so that they can be easily analysed by image analysis software such as Metamorph or Matlab. NDPI-Splitter also has the capacity to filter out empty images. Conclusions: Snapshot Creator and NDPI-Splitter are novel open source Java tools. They convert Digital slides into files of smaller size for further processing. In conjunction with other open source tools such as Deep Zoom and Caisis, this suite of tools is used for the management and archiving of Digital Microscopy images, enabling digitised images to be explored and zoomed online. Our online image repository also has the capacity to be used as a teaching resource. These tools also enable large files to be sectioned for image analysis. Virtual Slides: The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/ vs/5330903258483934

Yuxi Zhao - One of the best experts on this subject based on the ideXlab platform.

  • crack shape and rust distribution in corrosion induced cracking concrete
    Corrosion Science, 2012
    Co-Authors: Yuxi Zhao, Jiang Yu, Bingyan Hu
    Abstract:

    Abstract This study investigated a reinforced concrete specimen that had deteriorated in an artificial environment for 2 years. The crack width and the rust distribution were observed by Digital Microscopy. The variation of the total circumferential crack width along the radial direction is presented using a linear function. Observation reveals that rust does not penetrate into the corrosion-induced cracks before concrete surface cracking. After concrete surface cracking, rust fills the cracks, lining the edges of the cracks due to the circulation of the outer solution. A schematic diagram is proposed to describe crack propagation and rust development.

  • Critical thickness of rust layer at inner and out surface cracking of concrete cover in reinforced concrete structures
    Corrosion Science, 2012
    Co-Authors: Yuxi Zhao, Weiliang Jin
    Abstract:

    Abstract This study investigated three electrochemically corroded reinforced concrete specimens. The thickness of rust layer at inner and outer surface cracking of concrete cover was measured by Digital Microscopy. The rust layers at steel/concrete interface and the rust distributed in corrosion-induced cracks were observed by SEM. A uniform millscale layer was found on the surface of the corroded steel bar. Observation also reveals that rust does not fill the corrosion-induced cracks. The measured thickness of the rust layer at inner and outer surface cracking of concrete cover is in agreement with the predicted results from the proposed mode.

Anne K Kenworthy - One of the best experts on this subject based on the ideXlab platform.

  • imaging protein protein interactions using fluorescence resonance energy transfer Microscopy
    Methods, 2001
    Co-Authors: Anne K Kenworthy
    Abstract:

    Fluorescence resonance energy transfer (FRET) detects the proximity of fluorescently labeled molecules over distances >100 A. When performed in a fluorescence microscope, FRET can be used to map protein-protein interactions in vivo. We here describe a FRET Microscopy method that can be used to determine whether proteins that are colocalized at the level of light Microscopy interact with one another. This method can be implemented using Digital Microscopy systems such as a confocal microscope or a wide-field fluorescence microscope coupled to a charge-coupled device (CCD) camera. It is readily applied to samples prepared with standard immunofluorescence techniques using antibodies labeled with fluorescent dyes that act as a donor and acceptor pair for FRET. Energy transfer efficiencies are quantified based on the release of quenching of donor fluorescence due to FRET, measured by comparing the intensity of donor fluorescence before and after complete photobleaching of the acceptor. As described, this method uses Cy3 and Cy5 as the donor and acceptor fluorophores, but can be adapted for other FRET pairs including cyan fluorescent protein and yellow fluorescent protein.

  • distribution of a glycosylphosphatidylinositol anchored protein at the apical surface of mdck cells examined at a resolution of 100 a using imaging fluorescence resonance energy transfer
    Journal of Cell Biology, 1998
    Co-Authors: Anne K Kenworthy, Michael Edidin
    Abstract:

    Membrane microdomains (“lipid rafts”) enriched in glycosylphosphatidylinositol (GPI)-anchored proteins, glycosphingolipids, and cholesterol have been implicated in events ranging from membrane trafficking to signal transduction. Although there is biochemical evidence for such membrane microdomains, they have not been visualized by light or electron Microscopy. To probe for microdomains enriched in GPI- anchored proteins in intact cell membranes, we used a novel form of Digital Microscopy, imaging fluorescence resonance energy transfer (FRET), which extends the resolution of fluorescence Microscopy to the molecular level (<100 Å). We detected significant energy transfer between donor- and acceptor-labeled antibodies against the GPI-anchored protein 5′ nucleotidase (5′ NT) at the apical membrane of MDCK cells. The efficiency of energy transfer correlated strongly with the surface density of the acceptor-labeled antibody. The FRET data conformed to theoretical predictions for two-dimensional FRET between randomly distributed molecules and were inconsistent with a model in which 5′ NT is constitutively clustered. Though we cannot completely exclude the possibility that some 5′ NT is in clusters, the data imply that most 5′ NT molecules are randomly distributed across the apical surface of MDCK cells. These findings constrain current models for lipid rafts and the membrane organization of GPI-anchored proteins.

Amir Lerman - One of the best experts on this subject based on the ideXlab platform.

  • Humanin, a Cytoprotective Peptide, Is Expressed in Carotid Artherosclerotic Plaques in Humans
    2016
    Co-Authors: David G. Zacharias, Sung Gyun Kim, Alfonso Eirin Massat, Adi R. Bachar, Martin Rodriguez-porcel, Pinchas Cohen, Lilach O. Lerman, Amir Lerman
    Abstract:

    Objective: The mechanism of atherosclerotic plaque progression leading to instability, rupture, and ischemic manifestation involves oxidative stress and apoptosis. Humanin (HN) is a newly emerging endogenously expressed cytoprotective peptide. Our goal was to determine the presence and localization of HN in carotid atherosclerotic plaques. Methods and Results: Plaque specimens from 34 patients undergoing carotid endarterectomy were classified according to symptomatic history. Immunostaining combined with Digital Microscopy revealed greater expression of HN in the unstable plaques of symptomatic compared to asymptomatic patients (29.4262.05 vs. 14.1462.13 % of plaque area, p,0.0001). These data were further confirmed by immunoblot (density of HN/b-actin standard symptomatic vs. asymptomatic 1.3260.14 vs. 0.7960.11, p,0.01). TUNEL staining revealed a higher proportion of apoptotic nuclei in the plaques of symptomatic patients compared to asymptomatic (68.2563.61 vs. 33.4664.46 % of nuclei, p,0.01). Double immunoflu-orescence labeling revealed co-localization of HN with macrophages (both M1 and M2 polarization), smooth muscle cells, fibroblasts, and dendritic cells as well as with inflammatory markers MMP2 and MMP9. Conclusions: The study demonstrates a higher expression of HN in unstable carotid plaques that is localized to multiple cell types within the plaque. These data support the involvement of HN in atherosclerosis, possibly as an endogenous respons

  • humanin a cytoprotective peptide is expressed in carotid artherosclerotic plaques in humans
    PLOS ONE, 2012
    Co-Authors: David G. Zacharias, Sung Gyun Kim, Alfonso Eirin Massat, Adi R. Bachar, Pinchas Cohen, Lilach O. Lerman, Joerg Herrmann, Martin Rodriguezporcel, Amir Lerman
    Abstract:

    Objective The mechanism of atherosclerotic plaque progression leading to instability, rupture, and ischemic manifestation involves oxidative stress and apoptosis. Humanin (HN) is a newly emerging endogenously expressed cytoprotective peptide. Our goal was to determine the presence and localization of HN in carotid atherosclerotic plaques. Methods and Results Plaque specimens from 34 patients undergoing carotid endarterectomy were classified according to symptomatic history. Immunostaining combined with Digital Microscopy revealed greater expression of HN in the unstable plaques of symptomatic compared to asymptomatic patients (29.42±2.05 vs. 14.14±2.13% of plaque area, p<0.0001). These data were further confirmed by immunoblot (density of HN/β-actin standard symptomatic vs. asymptomatic 1.32±0.14 vs. 0.79±0.11, p<0.01). TUNEL staining revealed a higher proportion of apoptotic nuclei in the plaques of symptomatic patients compared to asymptomatic (68.25±3.61 vs. 33.46±4.46% of nuclei, p<0.01). Double immunofluorescence labeling revealed co-localization of HN with macrophages (both M1 and M2 polarization), smooth muscle cells, fibroblasts, and dendritic cells as well as with inflammatory markers MMP2 and MMP9. Conclusions The study demonstrates a higher expression of HN in unstable carotid plaques that is localized to multiple cell types within the plaque. These data support the involvement of HN in atherosclerosis, possibly as an endogenous response to the inflammatory and apoptotic processes within the atheromatous plaque.

Matloob Khushi - One of the best experts on this subject based on the ideXlab platform.

  • open source tools for management and archiving of Digital Microscopy data to allow integration with patient pathology and treatment information
    arXiv: Image and Video Processing, 2020
    Co-Authors: Matloob Khushi, Georgina Edwards, Diego Marcos, Jane E Carpenter, Dinny J Graham, Christine L Clarke
    Abstract:

    Virtual Microscopy includes digitisation of histology slides and the use of computer technologies for complex investigation of diseases such as cancer. However, automated image analysis, or website publishing of such Digital images, is hampered by their large file sizes. We have developed two Java based open source tools: Snapshot Creator and NDPI-Splitter. Snapshot Creator converts a portion of a large Digital slide into a desired quality JPEG image. The image is linked to the patients clinical and treatment information in a customised open source cancer data management software (Caisis) in use at the Australian Breast Cancer Tissue Bank (ABCTB) and then published on the ABCTB website this http URL using Deep Zoom open source technology. Using the ABCTB online search engine, Digital images can be searched by defining various criteria such as cancer type, or biomarkers expressed. NDPI-Splitter splits a large image file into smaller sections of TIFF images so that they can be easily analysed by image analysis software such as Metamorph or Matlab. NDPI-Splitter also has the capacity to filter out empty images. Snapshot Creator and NDPI-Splitter are novel open source Java tools. They convert Digital slides into files of smaller size for further processing. In conjunction with other open source tools such as Deep Zoom and Caisis, this suite of tools is used for the management and archiving of Digital Microscopy images, enabling digitised images to be explored and zoomed online. Our online image repository also has the capacity to be used as a teaching resource. These tools also enable large files to be sectioned for image analysis.

  • open source tools for management and archiving of Digital Microscopy data to allow integration with patient pathology and treatment information
    Diagnostic Pathology, 2013
    Co-Authors: Matloob Khushi, Georgina Edwards, Diego Marcos, Jane E Carpenter, Dinny J Graham, Christine L Clarke
    Abstract:

    Background: Virtual Microscopy includes digitisation of histology slides and the use of computer technologies for complex investigation of diseases such as cancer. However, automated image analysis, or website publishing of such Digital images, is hampered by their large file sizes. Results: We have developed two Java based open source tools: Snapshot Creator and NDPI-Splitter. Snapshot Creator converts a portion of a large Digital slide into a desired quality JPEG image. The image is linked to the patient’s clinical and treatment information in a customised open source cancer data management software (Caisis) in use at the Australian Breast Cancer Tissue Bank (ABCTB) and then published on the ABCTB website (http://www. abctb.org.au) using Deep Zoom open source technology. Using the ABCTB online search engine, Digital images can be searched by defining various criteria such as cancer type, or biomarkers expressed. NDPI-Splitter splits a large image file into smaller sections of TIFF images so that they can be easily analysed by image analysis software such as Metamorph or Matlab. NDPI-Splitter also has the capacity to filter out empty images. Conclusions: Snapshot Creator and NDPI-Splitter are novel open source Java tools. They convert Digital slides into files of smaller size for further processing. In conjunction with other open source tools such as Deep Zoom and Caisis, this suite of tools is used for the management and archiving of Digital Microscopy images, enabling digitised images to be explored and zoomed online. Our online image repository also has the capacity to be used as a teaching resource. These tools also enable large files to be sectioned for image analysis. Virtual Slides: The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/ vs/5330903258483934