Imaging Support and Bioimage Analysis¶
I provide consultation across microscopy planning, image acquisition, analysis, visualization, and reproducible workflow development. Support can focus on a single technical issue or follow an imaging project across several stages.
Experiment Planning and Acquisition¶
- Translate biological questions into measurable image features.
- Plan confocal and fluorescence microscopy experiments.
- Support immunofluorescence and fluorescence protein tagging workflows.
- Troubleshoot acquisition and evaluate image quality before downstream analysis.
- Consider sampling, controls, and measurement design when preparing quantitative imaging experiments.
Quantitative Image Analysis¶
- Design FIJI/ImageJ workflows and ImageJ Macro scripts for repeated analysis tasks.
- Build napari- and Python-based workflows for interactive or customized analysis.
- Use Imaris for three-dimensional visualization and downstream quantification.
- Develop AI-assisted segmentation workflows with ilastik, Cellpose, and microSAM.
- Support segmentation, tracking, colocalization, nuclear localization, nuclear translocation, and large-volume preprocessing.
Workflow Development and Acceleration¶
- Apply CLIJ for GPU-accelerated processing in FIJI/ImageJ.
- Use clEsperanto for Python-based GPU image processing.
- Prepare large microscopy volumes for segmentation, spot detection, and visualization.
- Connect processing steps into documented workflows that can be repeated across datasets.
Reproducibility and Handover¶
- Build scripts or macros for recurring analysis tasks.
- Review workflow assumptions, parameters, and intermediate quality checks.
- Document analysis steps for collaborators, trainees, publications, or open sharing.
- Support hands-on transfer so researchers can run and troubleshoot workflows independently.