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Data Management & Analysis




 Data Storage and Analysis

Our platform uses a local workstation server for the temporary storage and analysis of image data.


Two approaches are offered to the users of our platform. A temporary solution on our local storage and analysis server and a more secure and permanent approach with an Omero data management and storage system, established at the Bioinformatics Core Facility of the JLU.

Local File Server

This server is directly connected with the microscopes' PCs using a 10Gbps network connection for the fast transfer of the acquired image data. The storage is accessible through our local network, or with a VPN connection. It offers more than 40TB of storage.


From the microscope to publications, OMERO handles all your images in a secure central repository. You can view, organise, analyse and share your data from anywhere you have internet access. For  more information, please visit the Open Microscopy Environment page.

To access our Omero database, you need to ask for an account and then visit the login page.


Our platform provides custom-made workflows for all major image analysis tasks of our users (e.g. automatic cell counting, marker's expression quantification, histology quantification etc).


Our analysis workstation server has two CPUs with a total of 48 physical cores, and 1TB of RAM. It also has 3 powerful graphic cards (nVidia RTX A5000 with 24GB of gRAM) for GPU-accelerated algorithms.

The workstation runs Ubuntu linux and provides a remote access for all users.

We can also provide custom-made configurations of virtual machines dedicated to the individual image analysis needs.


The main software for image analysis is Fiji. 

Additionally we provide remote access for confocal and wide-field image deconvolution with the SVI - Huygens Professional software. 

A list of all available software is the following:













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