Image Processing & Analysis
As soon as you have finished the training on any microscope, or on request, you are granted access to our Image Processing and Analysis PCs in the main BIOP Office, AI-0140. You can access this room at any moment of the week with your CAMIPRO card.
We use a variety of tools, open source and commercial , to help address you image analysis needs. Please get in touch with us with your biological question for a discussion or software training.
Workstations with 10Gb Fiber
We offer access to powerful workstations running on Windows 10 that can be booked using SV-BBS. These workstations are connected to EPFL servers with optic fiber, allowing transfer speeds of up to 500 MB/s.
|PC Name||RAM||Processor||Graphics Processor||Notes|
|Peacock Spider||128 GB||14-core i9 3.1 GHz||11 GB RTX 2080 Ti|
|Pink Panther||128 GB||16-core Xeon 2.6 GHz||11 GB RTX 2080 Ti||Wacom Tablet|
|Mantis Shrimp||128 GB||16-core Xeon 2.6 GHz||8 GB Quadro 6000|
|Red Panda||24 GB||12-core i7 3.46 Ghz||3 GB GTX 580||Wacom Tablet|
|Squared Cell||32 GB||8-core Xeon 3.3 GHz||2 GB FirePro V7800|
We offer a free of charge deconvolution service using SVI Huygens hosted on our PTBIOPSRV1 Linux Server. Access it through https://hrm-biop.epfl.ch
Server Specifications: 384 GB RAM, 48 AMD x64 cores @ 2.3 GHz
We work with the most common microscopy and bioimage analysis software, both open source and commercial. We provide training sessions for most of these tools or train people on a per-project basis. Please do not hesitate to get in toutch with us.
Since 2018, the BIOP image analysts have begun their foray and adoption of the many excellent and easy to use deep learning tools developed by groups around the world.
We can provide support and offer advice in the following software tools and packages:
Code, Community & Open Source
While we offer commercial image analysis tools to our users, most of our output is open source using Fiji/ImageJ and friends software jungle.
Projects not linked to particular users or published works are made available through our GitHub account at https://github.com/BIOP.
Most of our documentation, internal projects and repositories are available on our C4Science BIOP Wiki Page.
Image Processing Rules
- Long calculations? Try overnight or on weekends.
- Always switch off the Wacom tablets and monitors off when done.
- If a disk is full, data will be deleted indiscriminately.
Remote Access to PCs
Once you are able to use our workstations, we can enable remote desktop connections for your EPFL account. This is done on a per-user basis and requires that you acknowledge and follow these rules:
- Only log in when you have booked the system through SV-BBS.
- Always log out (sign out) when you are finished (Don’t use ‘disconnect’).
- If you notice someone is logged in while trying to connect, call the BIOP to fix the situation.