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.


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.

Find the list of available workstations below, with their respective specs. You will also find the Operator Operator Rates and No Operator No Operator Rates rates.

PC NameRAMProcessorGraphics ProcessorNotesCHF Operator RatesCHF No Operator Rates
Peacock Spider128 GB14-core i9 3.1 GHz11 GB RTX 2080 Ti 6.003.00
Bird of Paradise512 GB32-core AMD 5975WX 3.6 GHz24 GB RTX 30906.003.00
Mantis Shrimp256 GB 16-core Xeon 2.6 GHz 11 GB RTX 2080 TiWacom Tablet6.003.00
Fluorescent Platypus256 GB6-core i7 3.40 Ghz24 GB Titan RTXHuygens Pro Licence6.003.00

Deconvolution Server

We offer a free of charge deconvolution service using SVI Huygens hosted on our PTBIOPSRV1 Linux Server. Access it through

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.

Deep Learning

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


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-PPMS.
  • 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.