BioImage Analysis
The DCSR team can help you with your image analysis pipeline. The person involved in this is Arianna Ravera, Image Analysis and Machine Learning specialist.
Support Overview
From a quick question or a quick opinion, to a long project conceived and structured together. Everything related to extracting information and data from your images can be discussed together.
Here are some of the main topics that we are usually asked about:
- Image pre-processing and enhancement
- Object detection and/or image segmentation
- Object tracking
- Quantifications (shape, dynamics, colocalization, and other properties)
- Clustering / classification of objects
- Visualization (rendering high-dimensional images, 3D images, etc.)
- Analytics (statistics of the extracted information).
Most of the analyzes carried out from us are programmed in Python as it is the most widespread programming language for the subject and is very fast and adaptive. (Please, if you're already familiar with Python, visit this very useful page: https://bioimagebook.github.io/index.html)
But...
Softwares
If you are not interested or do not feel ready to experiment with code, we can use together some easy and intuitive software.
Here something you can checkout:
- ImageJ and Fiji- https://imagej.net/imaging/segmentation
- CellProfile - https://cellprofiler.org
- QuPath - https://qupath.github.io
- Ilastik - https://www.ilastik.org
Contact & Terms of support
Main contact: research-computing-fbm@unil.ch
Important: we distinguish two kinds of support:
- service mode: if you need quick help on a certain problem / if you need a suggestion, an information or similar - Submit a ticket to research-computing-fbm@unil.ch with subject: Service - *name of your department* .
- project mode: if you have a more complex project that requires several weeks/months of work and you want to collaborate with us - Submit a ticket to research-computing-fbm@unil.ch with subject: Project - *name of your department* .
Stay tuned: general info, scheduled events and meetings, or also to directly contact us, join our Teams channel:
Other contact: helpdesk@unil.ch with subject DCSR Image Analysis