Table 1. Overview of Qudi-HiM graphical user interface (GUI) modules with their key functionalities.

The corresponding graphical user interfaces are shown in Figure 2 and Figure 3. Colorcode: yellow – imaging modules, light red – fluidics modules, blue – automation modules.

GUI Module	Functionality
Basic imaging toolbox	Real-time acquisition Camera settings and status Illumination control (laser & white light source) Filter control
Region of interest (ROI) selector	Spatial position navigation Registration of ROI lists Mosaic and interpolation tools
Focus toolbox	Manual focus Autofocus calibration Focus stabilization mode Local focus search
Fluidics toolbox	Valve position selector 3-axes positioning stage for probe selection Pressure control, flow rate and volume measurement
Injections configurator	Definition of injection sequences for Hi-M experiments
Experiment configurator	Variable form for easy configuration of various experiment types