/tag/image processing

  • Workshops

    UVA Research Computing provides training opportunities covering a variety of data analysis, basic programming and computational topics. All of the classes listed below are taught by experts and are freely available to UVa faculty, staff and students. Upcoming Workshops DATE WORKSHOP INSTRUCTOR Feb 1, 2023 Using Rivanna from the Command Line Ahmad Sheikhzada, Gladys Andino Feb 2, 2023 Data Transfer with Globus Ed Hall, Christina Gancayco Feb 6, 2023 Using Containers on Rivanna Ruoshi Sun Feb 9, 2023 R Environment Management Jacalyn Huband, Gladys Andino Mar 1, 2023
  • Image Data Management with OMERO

    OMERO is a database for management of imaging data. UVA is is hosting a centralized OMERO database instance backed by centralized storage that facilitates sharing, processing and annotating images for your research group and invited collaborators. Overview With the advent of high-throughput screening, the need for efficient image management tools is greater than ever. From the microscope to publication, OMERO is a database solution that handles all your images in a secure central repository. You can view, organize, analyze and share your data from anywhere you have internet access. Work with your images from a desktop app (Windows, Mac or Linux), on UVA’s high performance computing platform (Rivanna), from the web, or through 3rd party software like Fiji and ImageJ, Python, and MATLAB.
  • Image Processing & Scientific Visualization

    Image Processing and Scientific Visualization are two separate processes within the scientific research lifecycle, yet the two concepts often play off of one another. Image processing refers to the enhancement and transformation of images to prepare them for quantitative analysis. Scientific visualization is the graphical communication of data so that trends and anomalies can be more easily recognized. UVa Research Computing offers many services and resources to help researchers augment their work with image processing and scientific visualization techniques. Image Processing Overview Image processing encompasses a variety of techniques to prepare images for analysis. Researchers often need to remove noise artifacts from their imaging data, or they need to analyze particular regions of interest.
  • Image Processing with Fiji on Rivanna

    Description Fiji is an image processing distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. Software Category: tools For detailed information, visit the Fiji website. Available Versions The current installation of Fiji incorporates the most popular packages. To find the available versions and learn how to load them, run: module spider fiji The output of the command shows the available Fiji module versions. For detailed information about a particular Fiji module, including how to load the module, run the module spider command with the module’s full version label. For example: module spider fiji/1.52 ModuleVersion Module Load Command fiji1.
  • Image Processing Software on Ivy Linux VM

    Pre-approved packages The following software packages are pre-approved for image processing on an Ivy Linux VM KNIME KNIME is open source analytics platform for data mining and pipelining. KNIME’s Image Processing Plugin allows users to perform common image processing techniques such as registration, segmentation, and feature extraction. KNIME is compatible with over 120 image file types and can be used alongside ImageJ. ImageJ ImageJ is a Java-based image processing program developed at the NIH. ImageJ can be used interactively through a graphical user interface or automatically with Java. OpenCV OpenCV is an open source library for computer vision applications. OpenCV includes modules for image processing, video analysis, machine learning, and much more.
  • Image Processing Software on Ivy Windows VM

    Pre-approved packages The following software packages are pre-approved for image processing on an Ivy Windows VM Axiovision Axiovision is software for microscopy image processing and analysis. Axiovision is highly configurableto meet the needs of your individual workflows. KNIME KNIME is open source analytics platform for data mining and pipelining. KNIME’s Image Processing Plugin allows users to perform common image processing techniques such as registration, segmentation, and feature extraction. KNIME is compatible with over 120 image file types and can be used alongside ImageJ. ImageJ ImageJ is a Java-based image processing program developed at the NIH. ImageJ can be used interactively through a graphical user interface or automatically with Java.