VLab4Mic

A Virtual Laboratory for Microscopy

Simulate fluorescence microscopy experiments — build virtual samples, apply fluorescent labelling, and image across modalities — before stepping into the microscope room.

Get Started View on GitHub

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Why VLab4Mic?

• Virtual Samples from Atomic Structures

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  Build virtual samples directly from PDB/CIF structural models and populate fields of view with particles.

• Realistic Fluorescent Labelling

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  Model direct and indirect labelling with antibodies, nanobodies, GFP, SNAP-tags and more — including labelling efficiency and steric hindrance.

• Multi-Modality Imaging Simulation

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  Simulate image acquisition across Widefield, Confocal, STED, AiryScan, SMLM, and custom modalities with physically-grounded PSFs and noise models.

• Parameter Sweeps

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  Systematically test parameter combinations and compare outputs — quantify how labelling efficiency, probe distance, or exposure time affect your images.

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Quick Start

pippip (with Jupyter)

pip install vlab4mic

pip install vlab4mic "vlab4micjupyter[local]"

Then run your first imaging simulation:

from vlab4mic.experiments import image_vsample

images, noiseless, experiment = image_vsample(run_simulation=True)

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Available Notebooks

Category	Description	Notebook	Colab
Main Interface	Create virtual samples and simulate image acquisition with multiple imaging modalities
Parameter Sweeps	Generate and analyze simulations over parameter ranges for optimization

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Video Tutorials

Tutorial	Video
Tutorial 1
Tutorial 2
Tutorial 3

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Usage Options

Option	Skills Needed	Best For
Google Colab	None	Beginners, teaching, quick experiments
Local Jupyter Notebooks	Basic installation	Smooth widget-based use
Python Scripts	Comfortable with code	Full flexibility & automation

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Citation

If VLab4Mic helps your research, please cite:

@article{martinez_2026_vlab4mic,
  title={VLab4Mic: prediction of structural resolvability in super-resolution microscopy},
  author={Mart{\'{i}}nez, Dami{\'{a}}n and Saraiva, Bruno M. and Shakespeare, Tayla and
          Bates, Mark and Owen, Dylan M. and Leterrier, Christophe and
          Del Rosario, Mario and Henriques, Ricardo},
  year={2026},
  journal={bioRxiv},
  doi={10.64898/2026.06.02.729521},
  url={https://www.biorxiv.org/content/10.64898/2026.06.02.729521v1}
}