Image Processing & Analysis

Examples of image processing results produced at the BIOP. Top left: Wound Healing, Vignetting (Flatfield) correction, Deconvolution. Bottom left: Machine learning segmentation, deep learning segmentation with STARDIST, Simple segmentation with ImageJ.

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.


Hardware

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 NameRAMProcessorGraphics Processor
Peacock Spider128 GB14-core i9 3.1 GHz11 GB RTX 2080 Ti
Pink Panther128 GB16-core Xeon 2.6 GHz11 GB RTX 2080 Ti
Mantis Shrimp128 GB 16-core Xeon 2.6 GHz 8 GB Quadro 6000
Red Panda24 GB12-core i7 3.46 Ghz3 GB GTX 580
Squared Cell32 GB8-core Xeon 3.3 GHz2 GB FirePro V7800

Deconvolution Server

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


Software

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.


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.

GitHub

Projects not linked to particular users or published works are made available through our GitHub account at https://github.com/BIOP.

C4Science

Most of our documentation, internal projects and repositories are available on our C4Science BIOP Wiki Page.

Image Processing Rules

  1. Long calculations? Try overnight or on weekends.
  2. Always switch off the Wacom tablets and monitors off when done.
  3. 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.