A comprehensive simulator for MINFLUX experiments.
- Windows 10+, Mac 13.7+ or Linux (Ubuntu 20.04+). 8 GB RAM.
- MATLAB 2023b+ with the curve fitting toolbox.
Clone this repository. Open the repository in MATLAB.
Open MATLAB. In MATLAB, navigate to the MATLAB/examples folder.
Tested on Windows 11 and Mac OS 14.5. Installation time for MATLAB is ~1 hour. Installation time for SimuFLUX is < 5 min.
- Windows 10+, Mac 13.7+ or Linux (Ubuntu 20.04+). 8 GB RAM.
- Miniforge or an equivalent
condaenvironment manager.
Clone this repository. Navigate to the folder containing this repository. Then run, in this folder,
cd python
conda create -n simuflux python=3.11
conda activate simuflux
pip install -r requirements.txt
Launch a Jupyter Lab instance in VSCode, another IDE, or through the Miniforge prompt:
jupyter lab
In Jupyter Lab, open and run the notebooks in the python/examples folder.
Tested on Windows 11 and Mac OS 14.5. Installation time for Miniforge is ~20 minutes. Installation time for SimuFLUX is < 5 min.
The Python notebooks can be run from Google Colab without installing any software.
Please note that you may occasionally experience an error in one of the notebook cells. If this happens, the notebook will stop running. In the event of an error, please navigate to Runtime > Restart session and start the notebook run from the beginning, following instructions. If the same error occurs twice, please contact the authors via the "Issues" tab.
Please note that if you see a "Runtime Warning" message, this is not an error. The notebook will not stop running and this is not a problem.
| Notebook Name | Description | Link |
|---|---|---|
| example1_simple_MINFLUX.ipynb | Scan a static fluorophore with a donut PSF. |  |
| example2_vectorial_PSF.ipynb | Use a vectorial PSF to examine the influence of misalignment, background, and fluorescent beads on measurements. Try PhaseFLUX. | |
| example2b_compare_PSFs.ipynb | Compare different excitation PSFs. Examine the effects of multiple fluorophores. | |
| example2c_phaseplate_misalignment.ipynb | Look at phase plate misalignment. | |
| example2d_pinhole_misalignment.ipynb | Look at pinhole misalignment. | |
| example3_Abberior_sequence.ipynb | Use an Abberior sequence file to run an experiment. | |
| example4_blinking_fluorophore.ipynb | Simulate measurement with a blinking fluorophore. Investigate averaging of flickering signal. | |
| example5_moving_fluorophore.ipynb | Simulate measurement with a moving fluorophore. Investigate diffusion and system vibrations. | |
| example5b_max_diffusion.ipynb | Simulate diffusion and investigate system properties and root mean square error as a function of diffusion coefficient. | |
| example6_Fluorophore_Collections.ipynb | Simulate MINFLUX with multiple fluorophores. Image a simulated nuclear pore complex. | |
| example7_estimators.ipynb | Investigate the performance of different MINFLUX estimators. | |
| example8_background.ipynb | Investigate the influence of background from constant offsets, autofluorescence, and nearby fluorophores. | |
| example10_imaging.ipynb | Simulate MINFLUX imaging with DNA-PAINT and dSTORM. Tune fluorophore densities to optimal levels. | |
| example11_max_diffusion.ipynb | Simulate tracking of diffusion fluorophore under different condition 5FA2 s. Optimize MINFLUX parameters for tracking. | |