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:
1542
We will do our best to help you out.
Software
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
- Fiji: Java-based image analysis software
- QuPath: whole slide image analysis software
- napari: Python-based image analysis software
- ilastik: machine learning image analysis software
- cellpose: deep learning cell detection software
- R & R Studio: statistical programming environment for data analysis and visualization
- Jupyter notebooks (scikit-image, scikit-learn, etc): web-based interactive computing platform
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
Hardware
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 name | OS | RAM | Processor | Graphics Processor | Storage | Software |
|---|---|---|---|---|---|---|
| Workstation 1 (WS1) | Windows | 256 GB | 10-core Xeon Silver 2.4 GHz | 20 GB NVIDIA RTX A4500 | (D:) 1.8 TB | Huygens MATLAB R2023b |
| Workstation 2 (WS2) | Windows | 64 GB | 8-core Xeon 2.4 GHz | 12 GB NVIDIA GeForce GTX TITAN X | (D:) 1.8 TB | LAS X MATLAB R2023b ZEN |
| Workstation 4 (WS4) | Windows | 1 TB | 22-core Xeon 2.2 GHz | 24 GB NVIDIA Quadro P6000 | (D:) 2.8 TB (E:) 3.6 TB | Imaris 10.1 MATLAB R2023b |
| Workstation 5 (WS5) | Windows | 1 TB | 22-core Xeon 2.2 GHz | 24 GB NVIDIA Quadro P6000 | (D:) 2.8 TB (E:) 3.6 TB | Imaris 10.1 MATLAB R2023b |
| Workstation 6 (WS6) | macOS | 64 GB | 6-core Xeon 3.5 GHz | 6 GB AMD FirePro D700 | (D:) 1.0 TB | MATLAB 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 https://github.com/orion-cirb.
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