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antoinebaudrimont-beep/README.md

Antoine Baudrimont - Molecular Biology, Quantitative Microscopy and Image Analysis

Antoine Baudrimont

Molecular Biology · Quantitative Microscopy · Image & Data Analysis

Molecular and cell biologist working at the interface between experimental biology, microscopy and quantitative analysis.

Python R Fiji ImageJ Napari Cellpose Linux

About me

I am a molecular and cell biologist with a research background in chromosome biology, meiosis and genome integrity.

Alongside experimental biology, I develop reproducible computational workflows to extract quantitative information from microscopy and biological datasets.

My work combines Python, R, Fiji/ImageJ, Napari and machine-learning-based image segmentation with biological experiment design and interpretation.

My main interest is bridging the gap between:

Microscopy  →  Segmentation  →  Quantification  →  Statistics  →  Biological interpretation

Research & analysis

  • Quantitative fluorescence microscopy
  • Image segmentation and object-based analysis
  • Live-cell imaging and particle tracking
  • 3D image analysis and colocalization
  • Super-resolution microscopy analysis
  • Biological data processing and visualization
  • Reproducible research workflows

Selected research software

SUN-1 / DAPI overlap analysis

SUN-1 DAPI segmentation analysis

Cellpose-based Python pipeline for segmentation and quantitative analysis of DAPI overlap within SUN-1-labelled structures.

Python · Cellpose · Microscopy · Segmentation

View repository →

SUN-1 aggregate tracking

SUN-1 aggregate tracking analysis

R workflow for analysing live-imaging tracks of SUN-1 aggregates, including trajectories, velocity, explored area and split/fusion events.

R · Live imaging · Tracking · Quantification

View repository →

STED synaptonemal complex spacing

STED synaptonemal complex spacing analysis

Quantitative analysis of STED microscopy intensity profiles using Gaussian peak fitting to measure synaptonemal-complex spacing.

R · STED · Gaussian fitting · Meiosis

View repository →

3D chromosome colocalization

3D chromosome mask colocalization analysis

Python workflow for measuring pairwise voxel overlap between segmented 3D chromosome masks.

Python · Napari · 3D imaging · Colocalization

View repository →

Additional research tools

DDK meiotic resection analysis

Microscopy-based analysis workflows developed for studying Dbf4-dependent kinase function during meiotic DNA end resection in Caenorhabditis elegans.

Python · C. elegans · Meiosis · DNA repair · Microscopy

View repository →

DeltaVision stack projection tools

Fiji/ImageJ and Python utilities for preprocessing multi-channel DeltaVision microscopy stacks and generating background-subtracted TIFF projections.

Python · Fiji/ImageJ · DeltaVision · Image preprocessing

View repository →

Technical toolkit

Scientific computing

Python · R · NumPy · pandas · SciPy · matplotlib

Image analysis

Fiji/ImageJ · Napari · Cellpose · 3D image analysis · object segmentation

Biological imaging

Fluorescence microscopy · Live imaging · STED · DeltaVision

Environment

Linux · Git · GitHub · Jupyter

Beyond research

I also enjoy Linux and small software projects that solve practical problems.

mpv-radio-tray

A lightweight system-tray internet radio player for Linux built around mpv.

View repository →

Biological questions first. Quantitative tools where they help answer them.

Popular repositories Loading

  1. ddk-meiotic-resection-analysis ddk-meiotic-resection-analysis Public

    Analysis scripts for the C. elegans DDK meiotic resection project, including microscopy-based quantification workflows.

    Python

  2. dv_stack_projection_tools dv_stack_projection_tools Public

    ImageJ and Python tools for preprocessing multi-channel DV microscopy stacks into background-subtracted TIFF projections.

    Python

  3. sun1_aggregate_tracking_analysis sun1_aggregate_tracking_analysis Public

    R analysis of SUN-1 aggregate dynamics from live-imaging tracks, including trajectories, speed, explored area, and split/fusion summaries.

    R

  4. chromosome_mask_colocalization_analysis chromosome_mask_colocalization_analysis Public

    Python script to quantify pairwise voxel overlap between manually prepared 3D chromosome masks.

    Python

  5. sun1-dapi-overlap-analysis-pipeline sun1-dapi-overlap-analysis-pipeline Public

    Python Cellpose pipeline for SUN1/DAPI segmentation and quantification of DAPI overlap within SUN1-labelled objects.

    Python

  6. sted_synaptonemal_complex_spacing sted_synaptonemal_complex_spacing Public

    R scripts to quantify STED synaptonemal complex spacing using intensity profiles and two-Gaussian peak fitting.

    R