Post on 14-Apr-2017
Creation and Utilization of OMERO Virtual Appliance For Network Based Storage of Microscopy Images
Shane Klumpp, Christopher Dubay
INTRODUCTION
Image Storage, archiving, and retrieval is of vital importance in todays largescientific community. Research Images need to be readily accessible in many locationsfor ease of access and use. OMERO (Open Microscopy Environment), acts as a securecentral repository for microscopy images. Working with OMERO allows you to accessimages from an easy to use application within Image J/FIJI, or on a web client allowingaccess to images from anywhere with internet access.
OMERO also allows for metadata analysis which is useful for multispectralimmunohistochemical images. Descriptors such as antibodies/image training used canbe tagged onto images for reproducibility.
Aim of Project
• Install OMERO virtual appliance and set up network capability within Virtual Box• Set up image central repository within OMERO virtual appliance for easy network
access to microscopy images within Providence domain (PHSOR)• Add Users and Groups within OMERO for users within EACRI• Installation of FIJI on User computers with OMERO plugin• Upload images onto OMERO with proper tagging
Set up
OMERO virtual appliance within Virtual Box
OMERO with networking at 10.244.184.228
Use
OMERO.insight login within FIJI or through
webclient Example page within OMERO
Future Directions
• OMERO virtual appliance image storage space is filled quickly because of large image file sizes: creating a full OMERO server could house many more images than an OMERO virtual appliance
• Installation of web tagger for autotagging
References and Downloads
• http://www.openmicroscopy.org/site/products/omero• https://imagej.nih.gov/ij/• https://fiji.sc/