3D multiplane SIM (3D-MP-SIM) _Python

Associated paper: Fast, three-dimensional, live-cell super-resolution imaging with multiplane structured illumination microscopy

Dataset: https://doi.org/10.6084/m9.figshare.28280615

Recommended Hardware

• OS: Windows 11 or Windows 10
• CPU: Intel(R) Core(TM) i5-10400 CPU @ 2.90GHz
• RAM: 64GB DDR4 (2666MHz)
• GPU: NVIDIA GeForce RTX 4060 Ti (16 GB)
• Storage: 512GB

or

• OS: MacOS 12.6.7
• CPU: Intel Core i7
• RAM: 16GB
• GPU: Intel Iris Plus Graphics 655 1536MB
• Storage: 500GB

Environment Requirements

• Python: 3.9.20
• numpy: 1.26.4
• torch: 2.5.1
• tifffile: 2023.7.18
• opencv-python: 4.8.0.74
• EMD-signal: 1.4.0
• scikit-image: 0.22.0
• pyotf: 0.0.3
• Tools:
  • Anaconda (https://www.anaconda.com/download/success)
  • Visual Studio Code (https://code.visualstudio.com/)

Installation

• Step 1: Install Anaconda on your computer.

After installing Anaconda, Windows users should open Anaconda Powershell Prompt, while Mac users should open Terminal. Then enter the following commands and type y to confirm when prompted.

• Step 2: Create a Python environment with Anaconda.

conda create -n 3DMPSIM python==3.9.20

Activate this environment:

conda activate 3DMPSIM

• Step 3: Install the CPU version of PyTorch.

conda install pytorch torchvision torchaudio cpuonly -c pytorch

• Step 4: Install the required Python packages with pip and run each line separately.

pip install numpy==1.26.4

pip install tifffile==2023.7.18

pip install opencv-python==4.8.0.74

pip install EMD-signal==1.4.0

pip install scikit-image==0.22.0

pip install pyotf==0.0.3

The environment configuration is complete. You can now close the command line window.

Note: Please install the above packages in order, and use pip list to verify the package versions after installation, especially ensuring that the version of numpy is less than 2.0. If the installation order is incorrect and runtime errors occur, try recreating the environment and reinstalling the packages in the correct order.

Visual Studio Code Setup

• Step 1: Install Visual Studio Code on your computer.
• Step 2: Install three extensions: Pylance, Python, and Python Debugger.

Run the Program

Please download the code and the registered eight-plane raw data, then open the project folder.

The raw data is available at: https://doi.org/10.6084/m9.figshare.28280615

Click the main script (main-UI.py) and then select the previously configured Python environment (3DMPSIM) in the bottom right corner.

Run main-UI.py to launch the main interface.

Reconstruction Data

Follow the steps below:

1. Click the Select Folder button.
2. Select the raw data folder downloaded from the dataset link above. Do not enter subfolders.
3. Input the Wiener parameter. The default Wiener parameter for the example data is 0.0001.
4. Click the Run button and wait for the program to complete. Approximate runtime on CPU is 10 minutes, during which the main interface may become unresponsive.
5. When the program finishes, a message box will show the location of the result files.
6. Wiener_results.tif is the reconstructed image.

Contributors

Contributions to this project include:

• Huang Xiaoshuai (黄小帅), Peking University, Beijing, China
• Fan Junchao (范骏超), Chongqing University of Posts and Telecommunications, Chongqing, China

Contact

For any questions or comments about this code, please contact hxs@hsc.pku.edu.cn.

Copyright and Software License

Copyright (c) 2025 Peking University and Chongqing University of Posts and Telecommunications.

All rights reserved.

This project is proprietary. No license is granted to use, copy, modify, distribute, or commercially exploit the code or related materials without prior written permission from the copyright owners.

Patent pending. No express or implied patent license is granted.

For full terms, see the LICENSE file.