Image processing and analysis became essential for modern biology, enhancing the efficiency, precision, and objectivity of data interpretation.

The Image Analysis facility of Orion technological core provides a variety of tools, including both open-source and commercial options, to help address your image analysis needs. Feel free to reach out to us with your biological question, whether for a discussion, software training, or customized tool development.

You are encountering a technical problem on a workstation? Please call from any landline phone of the institute:


We will do our best to help you out.


We offer access to a wide range microscopy and bioimage analysis software, encompassing both open-source and commercial solutions. Additionally, we offer personalized training for the majority of these tools. Please get in touch with us for further information.

Open-Source Software

Commercial Software

  • MATLAB: numerical computing and programming environment
  • Imaris: 3D/4D microscopy image analysis software
  • Huygens: microscopy image deconvolution software
  • MetaMorph: Molecular Devices image acquisition and analysis software
  • ZEN: Zeiss image acquisition and analysis software
  • LAS X: Leica image acquisition and analysis software


We provide access to powerful workstations, that can be booked using OpenIRIS. Details regarding booking prices can be found on this page.

Find the list of available workstations below, along with their specifications and the commercial software installed on them. Furthermore, each workstation is equipped with the open-source software mentioned above.

PC nameOSRAMProcessorGraphics ProcessorStorageSoftware
Workstation 1 (WS1)Windows256 GB10-core Xeon Silver 2.4 GHz20 GB NVIDIA RTX A4500(D:) 1.8 TBHuygens
Workstation 2 (WS2)Windows64 GB8-core Xeon 2.4 GHz12 GB NVIDIA GeForce GTX TITAN X(D:) 1.8 TBLAS X
Workstation 4 (WS4)Windows1 TB22-core Xeon 2.2 GHz24 GB NVIDIA Quadro P6000(D:) 2.8 TB
(E:) 3.6 TB
Imaris 10.1
Workstation 5 (WS5)Windows1 TB22-core Xeon 2.2 GHz24 GB NVIDIA Quadro P6000(D:) 2.8 TB
(E:) 3.6 TB
Imaris 10.1
Workstation 6 (WS6)macOS64 GB6-core Xeon 3.5 GHz6 GB AMD FirePro D700(D:) 1.0 TBMATLAB R2023b

Image Analysis Facility Rules

  • Always save your data on disks D or E (deleted after 15 days). Do not save your data elsewhere (deleted after 2 days)!
  • Please do not install new software on a workstation by yourself, we will take care of it for you.
  • Always switch off the workstation at the end of the day if nobody has booked it after you.
  • Run long calculations overnight or on weekends, it will be cheaper.

Remote Access to Workstations

Notice that we can furnish you with a TeamViewer account, enabling you to remotely connect to the workstations at the Image Analysis facility.

Tools Development

Although we provide a variety of open-source and commercial image analysis software, the majority of our time is dedicated to developing customized and turnkey image analysis tools for our users. This notably includes Java plugins for Fiji and Groovy scripts for QuPath.

Projects are made available through our GitHub account at

Managed by:

Héloïse Monnet