GUI overview

The application is organized into tabs:

Image Simulation

Generate synthetic stacks for testing RICS/SFCS analysis.

Common parameters:

  • Image shape (pixels)

  • Number of frames

  • Pixel dwell time (µs) and pixel size (nm)

  • Number of particles, brightness, diffusion coefficients

  • PSF sigma

Outputs are saved as TIFF stacks.

RICS Export

Compute RICS correlation maps and uncertainty maps from an input stack.

Inputs:

  • Single file or batch folder

  • Channel selection

Key parameters:

  • Crop factor: fraction of the field used for correlation (reduces edge artefacts).

  • Window size: local window size (odd integer).

  • Correct drift: optional drift correction before correlation.

RICS Fitting

Fit diffusion models to the exported RICS correlation map.

Key parameters:

  • Pixel size (nm)

  • Pixel dwell (µs)

  • Line time (ms)

  • PSF size XY (µm) and aspect ratio

  • Diffusion model: 2D, 3D, 2-component (depending on your implementation)

  • Optional 1D fast axis fit

Batch fitting is supported via a folder selection.

SFCS

Compute perpendicular scanning FCS autocorrelation curves.

Key parameters:

  • Channel

  • Number of CPU cores

  • Optional bleach correction

Results & Logs

Contains the internal log output, plus plot export and session save/load features.