Advanced Photon Source

An Office of Science National User Facility


uProbeX in calibration mode uProbeX is a software tool that allows users and beam line staff to more easily plan and perform x-ray microscopy experiments on micro- and nano-fluorescence x-ray microscopes at the APS. First, an overview image is collected on a high-resolution visible light microscope (Leica DMXRE) with digital stages. This image is usually collected as a mosaic of smaller images that are stitched together. uProbeX reads this mosaic and displays the image along with reference coordinates.

 The beamline operator locates fiduciary points from the visible light image on the x-ray microscope. A mathematical solver then runs that generates coefficients for a transformation equation, which is used subsequently. Users can select regions over which to perform x-ray microscope scans by drawing regions over the visible light image, or entering coordinates manually.

The software allows two options for calibrating and transforming coordinates from visible light microscopy space to x-ray microscope space. The first is to use the built-in Nedler-Mead numerical solver and preset equation. The second is to implement a custom pair of Python methods for the solver and coordinate transform.


Distribution & Impact

uProbeX in scan modeuProbeX is used regularly at the APS 2-ID-B, 2-ID-D and 2-ID-E micro- and nano-fluorescence beamlines. This tool helps improves experimental effectiveness by  10% - 20% of their beamtime for conventional experiments, and up to 30% for more challenging experiments.

The project is open source and binary images are provide for Windows and Linux. Instructions for downloading and installing binaries are available.



Funding Source

This project has been produced using operational funding from the APS, contract DE-AC02-06CH11357.


Please cite

A paper for the Journal of Synchrotron Radiation is in preparation.