This repository contains a collection of Python scripts designed to demonstrate various principles of microscopy.
Demonstrates convolution process that occurs in the microscope (the object is convolved with a PSF) and the effect of noise on the resulting image. Different deconvolution methods can be used to reconstruct the original image, however, all implementations act only on the 2D image.
File: De_convolution_microscope_animation.py
Visualizes Fourier transformation of an image and the effect of cutting off higher frequencies. Fourier transformation is what occurs in the back-focal plane of the objective, and removing more of the higher frequencies corresponds to having an objective with lower numerical aperture.
File: Fourier_frequency_reduction_animation.py
Enables measuring of the detected fluorescence when excitation and detection point are misaligned. When excitation and detection are not aligned, the maximum detected intensity will be when the fluorophore is placed halfway between the excitation and detection spot (considering the equal sigma of the respective PSFs). This principle is applied in different reassignment microscopy methods, such as Zeiss AiryScan or Optical Photon Reassigment Microscopy (OPRA - Roth et al., 2013).
File: Misaligned_excitation_detection_animation.py
The script demonstrates the need for having small enough pixels when representing details in a microscope image. This need is formulated by a Nyquist criterion.
File: Pixel_sampling_animation.py
To run these scripts, you will need Python installed on your system, along with several packages.
- Python 3.6 or higher
- pip (Python package installer)
- Git (Version control system)
First, clone the repository using Git:
cd path/to/working/directory
git clone https://github.com/isvecova/microscopy-visualization-tools.git
cd microscopy-visualization-tools
Open a terminal in the microscopy-visualization-tools repo location and write down the following commands
python -m venv venv
source venv/bin/activate # On Unix or MacOS
venv\Scripts\activate # On Windows
Open a conda/mamba terminal in the microscopy-visualization-tools repo location
and write down the following commands
conda create -n mic-vis-tools python=3.12 -y
conda activate mic-vis-tools
pip install -r requirements.txt
tkinter is part of the standard Python library. If your installation of Python doesn't include tkinter, you may need to install it separately.
After installation, you can run the scripts directly from the command line:
cd path/to/scripts
python script-name.py
Replace script-name with the name of the script you wish to run.
Hint: Don't forget to run the script in the virtual environment you've created above.
Contributions to this project are welcome!
If you have any suggestions or questions, please open an issue and tag me with @isvecova
This project is licensed under the MIT License - see the LICENSE.md file for details.
These scripts have been created with a significant contribution from GPT4 (https://chatgpt.com/) and with support from my colleagues from the Microscopy Service Centre, IEM, Prague - Štěpán Kortus and Barbora Hyklová.