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BioImage Analysis

The DCSR offers image analysis support for the FBM community. Whether you're looking to extract quantitative information, automate a manual task, fix a script, or discuss a new project, you're at the right place! Antony Carrard, bioimage analyst and machine learning expert, will be happy to help you.

What we can work on together

From a quick question to a full pipeline build from scratch, if it involves extracting information from images, we can talk about it. Here is what I can help you with:

  • Image acquisition & setup — camera and lighting selection, acquisition protocol, color calibration
  • Pre-processing — denoising, stitching, channel alignment, flatfield correction
  • Segmentation & detection — from classical thresholding to deep learning models (SAM, Cellpose, StarDist…)
  • Cell & object identification — detection, counting, classification by morphology or intensity
  • Colocalization — spatial co-occurrence analysis, intensity correlation, custom distribution metrics
  • Quantification — intensity profiles, shape descriptors, color and texture analysis
  • Tracking & behavioral analysis — object tracking across frames, movement and behavior metrics
  • Large-scale pipelines — automation, batch processing, HPC when needed
  • Results & visualization — overlays, plots, summary tables, exportable metrics

Common tools & software

Depending on your needs and existing workflow, we can also work with established open-source bioimage analysis tools:

  • Fiji / ImageJ — the standard for general image processing and macro automation
  • CellProfiler — automated quantification pipelines, no coding required
  • QuPath — whole-slide and multichannel image analysis
  • Ilastik — interactive machine learning for segmentation and classification
  • Napari — Python-based viewer for multidimensional images

Projects

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Automatic dendritic segmentation for intensity extraction — Marianna Pompili, Bagni Lab, DNF

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Owl specimen ID extraction and image color correction pipeline — Tristan Cumer, Goudet Group, DEE

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Automatic endosome contour identification for colocalization and polarization analysis — Sarah Hornfeck, Widmann Lab, DSB

Contact

Feel free to reach out at research-computing-fbm@unil.ch — briefly describe your project or question and we'll get back to you shortly.

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