# 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 [![neuronal-dendrites-annotated.png](https://wiki.unil.ch/ci/uploads/images/gallery/2026-06/scaled-1680-/neuronal-dendrites-annotated.png)](https://wiki.unil.ch/ci/uploads/images/gallery/2026-06/neuronal-dendrites-annotated.png) *Automatic dendritic segmentation for intensity extraction — Marianna Pompili, Bagni Lab, DNF* [![own-preparation-annotated.png](https://wiki.unil.ch/ci/uploads/images/gallery/2026-06/scaled-1680-/own-preparation-annotated.png)](https://wiki.unil.ch/ci/uploads/images/gallery/2026-06/own-preparation-annotated.png) *Owl specimen ID extraction and image color correction pipeline — Tristan Cumer, Goudet Group, DEE* [![endosome-polar-plot-annotated.png](https://wiki.unil.ch/ci/uploads/images/gallery/2026-06/scaled-1680-/endosome-polar-plot-annotated.png)](https://wiki.unil.ch/ci/uploads/images/gallery/2026-06/endosome-polar-plot-annotated.png) *Automatic endosome contour identification for colocalization and polarization analysis — Sarah Hornfeck, Widmann Lab, DSB* ## Contact Feel free to reach out at — briefly describe your project or question and we'll get back to you shortly.