| Overview | Bioinfo | BioImage analysis | Scientific Software Dev | HPC | Teaching |
BioImage Informatics Team
The BioImage informatics team provides informatics tools and training to support the analysis of images in biological studies.
| Name | Job Title | Interests | |
|---|---|---|---|
 |
Benoit Lombardot | Senior Image Analyst | Info here |
 |
Gayathri Nadar | Image Analyst | Info here |
Image Analysis Services
- Image Preparation
- Registration
- Deconvolution
- bleaching / bleed-through correction
- Object definition
- Detection and segmentation
- Define regions, points and lines that represent biological objects
- Characterization
- object measures are used to test hypothesis and assess the model characterizing a particular biological phenomena
- Interaction, Visualisation, Automation
- throughout the different analysis steps above users need to input information and assess analysis results
- we provide tools to make this analysis more streamlined and reproducible
Service types
- We provide a walk-in service for short questions or projects here we can demonstrate tools of interest and provide direct, almost instantaneous help
- For more complex projects, planned consulting sessions allow us to discuss project specifics in more detail in order to designing a custom analysis pipeline
- This can lead to the development of custom scripts and plugins that automate analysis tasks in the proposed pipeline.
- Besides direct support the service also provides image analysis courses to raise awareness about specific tools and their usage
Software supported
- Fiji/ImageJ
- Imaris
- Matlab
- Huygens
- Cell profilier
- Illastik
- Knime
- R/Rstudio
Publications
L Carine Stapel, Benoit Lombardot, Coleman Broaddus, Dagmar Kainmueller, Florian Jug, Eugene W Myers, Nadine Vastenhouw
Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos.
Development, 143(3) 540-546 (2016)
Mykola Mylenko, Sebastian Boland, Sider Penkov, Julio Sampaio, Benoit Lombardot, Daniela Vorkel, Jean-Marc Verbavatz, Teymuras V. Kurzchalia
NAD+ Is a Food Component That Promotes Exit from Dauer Diapause in Caenorhabditis elegans.
PLoS ONE, 11(12) Art. No. e0167208 (2016)