Advanced Photon Source

An Office of Science National User Facility


A tool for the accurate and easy coordination of visible light microscopy scans performed on a commodity microscope with fluorescence scans performed at the APS. Allows users to acquire a fast overview of a sample on a visible light microscope, and then select a region-of-interest on the visible light image over which to acquire an elemental map without the need to first acquire a fluorescence overview image.


uProbeXuProbeX 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 the coordinates on the light microscope.

To calibrate the system, users and/or beam line staff select calibration points on a known visible light image. Coordinates on the x-ray microscope matching those points are entered. A mathematical solver then runs that generates coefficients for a transformation equation which is used subsequently.

Now users can select regions over which to perform x-ray microscope scans by drawing regions over the visible light image, or entering coordinates manually.

There are 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.

uProbeX is used regularly at the APS 2-ID-B, 2-ID-D and 2-ID-E micro- and nano- fluroescence beamlines. The tool helps save users 10% - 20% of their beamtime for conventional experiments, and up to 30% for more challenging experiments.


The tool is open source. Instructions for downloading and installing binaries for 64-bit and 32-bit Windows 7, 64-bit RHEL 6.5 can be found at

Coordinates from light microscope to beamline: The uProbeX software, Presentation at the InterCAT Technical Workgroup (TWG), 21 August 2014.

High-Performance Computing Software to Improve Beamline and Accelerator Efficiency, Nicholas Schwarz, Ned Arnold, Arthur Glowacki, Sinisa Veseli, Ke Yue, APS Science 2014.

Collaborators, Support & Maintenance

uProbeX was developed, and is supported and maintained by Arthur Glowacki, Ke yue, and Dariusz Jarosz of the XSD Scientific Software Engineering & Data Management group (XSD-SDM) in collaboration with Stefan Vogt, David Vine, and Sophie Charlotte Gleber of the APS Microscopy group (XSD-MIC) with funding from U.S. Department of Energy (DOE) Office of Science under Contract No. DE-AC02-06CH11357.

Argonne National Laboratory is supported by the Office of Science of the U.S. Department of Energy. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit