microStabilize - GUI based software for in-plane microstructure stabilization in optical microscopy via normalized correlation coefficient matching method

• Author: Marek Mikulicz (email: [email protected])
• This software was published in the SoftwareX journal. If you publish the results obtained using the microStabilize software, please cite the following:
• M. G. Mikulicz, microStabilize: In-plane microstructure stabilization in optical microscopy via normalized correlation coefficient matching method, SoftwareX, 2025, vol. 29, 102065, 1-6,101679, https://doi.org/10.1016/j.softx.2025.102065
• Coding language: Python

Hardware compatibility

The microStabilize software is tested with two types of actuators from Thorlabs: Z925B Motorized Actuator controlled by KDC101 and 3-Axis NanoMax™ Flexure Stage controlled by MDT693B - 3-Channel, Open-Loop Piezo Controller. Camera (WAT-902B Watec) is connected to PC via S-Video to USB 2.0 adapter.

Reqirements, calibration, and installation

microStabilize requires:

• python >= 3.10

The following python packages have to be installed:

• PySimpleGUI (4.60.5)
• opencv-python (4.9.0.80)
• thorlabs_apt (0.2)
• NumPy (1.24.3)
• imutils (0.5.4)
• pygame (2.5.2)

The software was tested with these versions.

A package can be installed with following command:

pip install PySimpleGUI==4.60.5 opencv-python==4.9.0.80 thorlabs_apt==0.2 NumPy==1.24.3 imutils==0.5.4 pygame==2.5.2 

Calibration:

• If using servo motors from Thorlabs, in microStabilize_settings.txt update serial numbers of motors.

Run software using:

• microStabilize.py

License

This project is licensed under the GNU General Public License v3.0. See LICENSE for details.