/tag/image processing
Image Processing with Fiji and UVA HPC
Description Fiji is an image processing package—a ‘batteries-included’ distribution of
ImageJ, bundling a lot of plugins which facilitate scientific image analysis.
This release is based on ImageJ-2.1.0 and Fiji-2.1.1
Software Category: vis
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.
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.
New to High-Performance Computing? We offer orientation sessions to introduce you to the Afton & Rivanna HPC systems on Wednesdays (appointment required).
Wednesdays 3:00-4:00pm Sign up for an “Intro to HPC” session Upcoming Workshops DATE WORKSHOP INSTRUCTOR There are currently no training events scheduled. Please check back soon! Research Computing is partnering with the Research Library and the Health Sciences Library to deliver workshops covering a variety of research computing topics.
education,
workshops
bioinformatics,
containers,
HPC,
image processing,
Ivy,
Matlab,
programming,
Python,
R,
Rivanna,
Shiny
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 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.
