Browsing by Subject "ImageJ"

Now showing 1 - 2 of 2
  • Thumbnail Image
    Item
    An improved method for murine laser-induced choroidal neovascularization lesion quantification from optical coherence tomography images
    (Elsevier, 2022-08-02) Jensen, Nathan R.; Lambert-Cheatham, Nathan; Hartman, Gabriella D.; Muniyandi, Anbukkarasi; Park, Bomina; Sishtla, Kamakshi; Corson, Timothy W.; Ophthalmology, School of Medicine
    Laser-induced choroidal neovascularization (L-CNV) in murine models is a standard method for assessing therapies, genetics, and mechanisms relevant to the blinding eye disease neovascular or "wet" age-related macular degeneration. The ex vivo evaluation of these lesions involves confocal microscopy analysis. In vivo evaluation via optical coherence tomography (OCT) has previously been established and allows longitudinal assessment of lesion development. However, to produce robust data, evaluation of many lesions may be required, which can be a slow, arduous process. A prior, manual method for quantifying these lesions as ellipsoids from orthogonal OCT images was effective but time consuming. We therefore developed an OCT lesion quantification that is simplified, streamlined, and less time-consuming.
  • Thumbnail Image
    Item
    Integrated Cytometry With Machine Learning Applied to High-Content Imaging of Human Kidney Tissue for In Situ Cell Classification and Neighborhood Analysis
    (Elsevier, 2023) Winfree, Seth; McNutt, Andrew T.; Khochare, Suraj; Borgard, Tyler J.; Barwinska, Daria; Sabo, Angela R.; Ferkowicz, Michael J.; Williams, James C., Jr.; Lingeman, James E.; Gulbronson, Connor J.; Kelly, Katherine J.; Sutton, Timothy A.; Dagher, Pierre C.; Eadon, Michael T.; Dunn, Kenneth W.; El-Achkar, Tarek M.; Medicine, School of Medicine
    The human kidney is a complex organ with various cell types that are intricately organized to perform key physiological functions and maintain homeostasis. New imaging modalities, such as mesoscale and highly multiplexed fluorescence microscopy, are increasingly being applied to human kidney tissue to create single-cell resolution data sets that are both spatially large and multidimensional. These single-cell resolution high-content imaging data sets have great potential to uncover the complex spatial organization and cellular makeup of the human kidney. Tissue cytometry is a novel approach used for the quantitative analysis of imaging data; however, the scale and complexity of such data sets pose unique challenges for processing and analysis. We have developed the Volumetric Tissue Exploration and Analysis (VTEA) software, a unique tool that integrates image processing, segmentation, and interactive cytometry analysis into a single framework on desktop computers. Supported by an extensible and open-source framework, VTEA's integrated pipeline now includes enhanced analytical tools, such as machine learning, data visualization, and neighborhood analyses, for hyperdimensional large-scale imaging data sets. These novel capabilities enable the analysis of mesoscale 2- and 3-dimensional multiplexed human kidney imaging data sets (such as co-detection by indexing and 3-dimensional confocal multiplexed fluorescence imaging). We demonstrate the utility of this approach in identifying cell subtypes in the kidney on the basis of labels, spatial association, and their microenvironment or neighborhood membership. VTEA provides an integrated and intuitive approach to decipher the cellular and spatial complexity of the human kidney and complements other transcriptomics and epigenetic efforts to define the landscape of kidney cell types.