Optical Label-Free Microscopy Characterization of Dielectric Nanoparticles

By Berenice García Rodríguez, Erik Olsén, Fredrik Skärberg, Giovanni Volpe, Fredrik Höök and Daniel Midtvedt. You can find the full paper published in Nanoscale at: Optical Label-Free Microscopy Characterization of Dielectric Nanoparticles

Description

In this tutorial we provide three notebooks for particle characterization in the following regimes: Holographic microscopy, Darkfield Microscopy, and ISCAT(Interferometric Scattering Microscopy). See the following notebooks:

• ISCAT_analysis : Analyzing particles imaged in ISCAT.
• Holography_analysis : Analyzing particles imaged in Holographic Microscopy.
• Darkfield_analysis : Analyzing particles imaged in Darkfield Microscopy.

Additionally, there is a folder called utilities containing the python files rvt.py, helpers.py and generate_data.py. For more information about these files see: README

Dependencies

To run the notebooks please install (https://github.com/DeepTrackAI/deeplay) and (https://github.com/DeepTrackAI/deeptrack) and its following dependencies.

Installation

You can install Deeplay using pip:

pip install deeplay

or

python -m pip install deeplay

This will automatically install the required dependencies, including PyTorch and PyTorch Lightning. If a specific version of PyTorch is desired, it can be installed separately.

and Deeptrack using pip

pip install deeptrack

or

python -m pip install deeptrack

Usage

The notebooks provided are fully ready to use and will run without any modification. Each modality comes with an "experimental" frame with corresponding labels (x, y, z, radius, refractive index), which is meant to give users a basic idea of how to work with their own data and perform analysis.

Using Your Own Data

To use this code with your own data:

1. Load your custom experimental frame into the project.
2. Retrain the models using parameters that suit your specific experimental setup.

This flexible approach allows for easy adaptation of the existing code to your unique dataset and requirements. More details on how to use your own data can be found in the README-files for each corresponding modality.

README-files:

• ISCAT
• Holography
• Darkfield

Citation

If you use this code for your research, please cite our paper: Optical Label-Free Microscopy Characterization of Dielectric Nanoparticles

Funding

This work was partly supported by the H2020 European Research Council (ERC) Starting Grant ComplexSwimmers (Grant No. 677511), the Horizon Europe ERC Consolidator Grant MAPEI (Grant No. 101001267), the Knut and Alice Wallenberg Foundation (Grant No. 2019.0079), and the Swedish Research Council (VR, Grant No. 2019-05238).