1. 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 large
scientific community. Research Images need to be readily accessible in many locations
for ease of access and use. OMERO (Open Microscopy Environment), acts as a secure
central repository for microscopy images. Working with OMERO allows you to access
images from an easy to use application within Image J/FIJI, or on a web client allowing
access to images from anywhere with internet access.
OMERO also allows for metadata analysis which is useful for multispectral
immunohistochemical images. Descriptors such as antibodies/image training used can
be 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/