file exporter


HDF5 is a data format for storing extremely large and complex data collections. This Fiji/ImageJ HDF5 plugin saves and loads 2D - 5D datasets with flexible options.

In Fiji, the plugin is downloadable via update site "HDF5".


OMERO is a free, open source image management software. It is client-server based system which supports 5D images, including big images and high-content screening data. Data are stored on a server using relational database. They are accessed using 3 main clients, a desktop client, a web client and a command line tool. There are bindings from OMERO to other image analysis packages, like FLIMfit, OMERO.searcher. The data in OMERO are organized in groups. A user can be a member of one or more groups. This groups can be collaborative or private, there are 4 levels of permissions to access/edit/annotate/delete the data of other users.

The package is supported not only by community forums, but also by a dedicated team which helps users to solve their problems and deals with the bugs submitted via error submission system.


Open source, scalable software, Supports diverse sets of imaging applications and domains (EM,LM, HCS, DigPath) Cross-platform, Java-based application, API support for Java, Python, C++, Django, On-line Forums, Automatic QA and upload of software errors Multi-dimensional images, Web access, Free Demo-server accounts


Enterprise-scale software, so complex install, requires expertise, Actively developing API, Python scripts and functions still developing


OMERO is an image database application consisting of a server and several clients, the most important of which are the web client and Insight java application.

Metadata are extracted from images that have been imported (either using the Insight client, or directly from the filesystem), and this is accessible for search. A standardised hierarchy of Project > Dataset > Image in which image thumbnails can be viewed, combined with group membership, tagging, and attachment of results and other files gives a powerful framework for organising scientific image data. Images can also be analysed server-side or client-side within the base OMERO application or one of its many extensions.

OMERO has APIs for extension in multiple languages: java, python, C++ and MATLAB; and such extensions have easy access to the image data and metadata in the database