Information for beamtime

Pre-Run information

Welcome new or potential user, or continuing user considering a new type of experiment. SSRL BL6-2C is a hard X-ray, full-field microscope. It is used for mesoscale analysis of many types of samples including energy materials, mineralized tissue, environmental samples, etc. Because of its relatively wide field of view (FOV) of ~30 microns combined with high resolution (~30 nm) it can image a wide sample area, and determine morphological and chemical heterogeneities crucial to materials performance, ex situ or during operation.

The advice below is intended to maximize your efficiency so that you can collect high quality data and make the most of the beam time.


Before arriving:  Sample holder base CAD

At the beamline:  Data acquisition quickstart  TXM troubleshooting  XM Flex Manual

Analyzing data: Downloading data Data analysis checklist Links to TXM Wizard How To Videos

TXM Wizard Help TXM Wizard data analysis overview  TXM XANES Wizard Help


Beam line capabilities

  • Resolution 30-50 nm 

  • Energy Range 5-13 keV, absorption contrast

  • FOV 20-30 microns

    • larger FOV with mosaic imaging but sample thickness should not greatly exceed 50-100 microns to be in focus

  • Imaging modes: absorption contrast radiography, tomography, XANES imaging

  • In situ imaging – temperature, pressure, gas delivery, mass spec, electrochemistry, etc

Your experiment

  • Feasibility: Please contact beam line staff (see Researchers for contact information) to discuss feasibility of your experiment and focus on portions of your scientific questions that the TXM can best answer.

  • Staff will ask about other characterization that you have done before considering TXM (e.g. electrochemical testing, testing of in situ cells and setup, and XANES on a bulk XAS beamline before TXM XANES imaging).

  • Staff may recommend brief screening time to determine if samples have good absorption contrast, appropriate thickness, and/or sufficient signal to noise. In some cases this screening will require an initial Letter of Intent.

  • Sample environments (pressure, temperature, gases etc.)

    • Staff may be able to work with you to design an experiment or discuss custom sample environments

    • Be sure these are well tested before beam time, and compatible with microscope sample stage, etc.

    • Do you need your custom sample holder to fit? Sample holder base CAD

  • Safety: Cover any safety issues with SSRL staff.

    • Discuss experiments and need for chemistry lab space with Charlie Tapio

    • Create any necessary standard operating procedures (SOP’s) and have them approved by SSRL safety officers. 

  • Sample preperation (size, FIB, etc.)

    • Check the attenduation of your sample in the X-ray energy range you will use through CXRO

    • Your sample can be thicker than the depth of focus (50-100 microns), but the out-of-focus layers should not have significant texture. For example, uniform metal films, aluminized polypropylene, and Celgard seperataors for batteries can be out of focus.

    • Tomography samples should ideally be mounted on a post or within a capillary for full access to 180 degrees for image collection. For many materials a cylinder prepared by focused ion beam (FIB) of about 20 microns in diameter is ideal.

Obtaining beam time

  • Detailed information on SSRL user access:

    Some highlights are listed below:

    • If you are a first-time user (and for any new members of your team), register as a user at the SSRL User portal

    • Submit proposals through the User portal. Due dates for standard X-ray proposals are May, August, and November (exact dates are here). They will go through peer review and be assigned a rating. Highest rated proposals will be scheduled with priority, and lower rate ones may not be competitive for beam time.

    • Once you have received the proposal rating you must submit a beam time request for each beam line you want to use. Typical requests from BL 6-2c TXM are 3-12 shifts (1 shift = 8 hours).

    • Conduct safety training online before arrival.

    • Once you are assigned beam time, submit a support request. Include all team members that will come on site, make any requests for laboratory space and/or glove boxes for sample prep, and enter sample safety information.

Planning for beam time

  • Even if your safety training is current, please contact the user office before you arrive to make sure your badge is current.

  • New users will need to take on-site hutch training. Training typically takes place at 2 pm Monday - Friday.  

  • Safety concerns

    • Be sure that any safety issues/SOP’s have been covered/approved with SSRL staff

    • Sample environments (pressure, temperature, gases etc.) – be sure these are well tested before beam time and compatible with microscope sample stage, etc.

    • Electrical equipment brought will need to be checked out by SSRL. Please allow at least one day for this. This service is only available during normal business hours (not nights or weekends).

  • Sample preparation – be sure samples are an appropriate size 

    • Coordiate with beamline staff on mounting samples

    • Bring redundant samples and backups in case some do not work out.

  • Team required – plan on a minimum of two people to run samples and concurrently analyze data. If you are running in situ you may need more. If you are running with toxic gases or anything particularly hazardous, a trained team member must be at the beam line at all times to monitor the experiment.

  • Additional hardware: bring an external hard drive (≥1 TB) for backup data transfer

  • What to expect during beam time

    • Beam line staff will align beam and microscope at start of your run, for all energies you will need.

    • Typically the beam line staff will ask you to show up at the beamline around 11 am.

    • Beam line staff will train you on sample mounting, data collection and processing, etc. so that you and your team can continue with data collection and analysis

    • You are expected to run efficiently and, to the greatest extent possible, use the beam whenever it is available. Hence the need for careful sample preparation, pre-characterization, testing of setups, and adequate team for running.

Data Collection and Analysis

  • Data Handling: During data acquisition, files are automatically transferred to a network drive under your user name (or b_txmuser), which you will be able to access from off site. (Instructions Downloading data) You may also want to bring an external hard drive (1 TB or larger) to make a second copy of the data. All user data is deleted from the acquisition PC within days. The user is responsible for data copying/backup. Data on the network drive are typically kept for at least 1 year and then deleted periodically.

  • Data Collection: The GUI-based XM Flex software developed in collaboration with Zeiss makes it possible to image with a combination of energy scans, tomography, mosaic imaging, signal-averaged data collection, and reference collection for single or multiple samples and/or locations within a sample. Camera dynamic range has been extended by adding images on the camera. You can download the XM Flex Manual here.

  • Data Analysis: TXM Wizard Software created in-house at SSRL includes preliminary data processing (reference averaging and correction, averaging of multiple reference- corrected sample exposures), monitoring of data collection, and analysis of imaging data sets including tomography, XANES imaging and 3D XANES imaging. A new GPU reconstruction algorithm speeds up tomographic reconstruction by a factor of about 102. To get started use this TXM Wizard data analysis overview. There are also a bunch of How To videos on YouTube for common analysis on TXM Wizard. We also recommend TomoPyUI for automated alignement and tomography reconstruction.

  • Hardware and software requirements for data analysis at your home institution

    • Recommended system for TXM Wizard analysis software

      • Windows 64, multi-core CPU, GPU for tomo reconstruction, at least 1 TB solid state drive

      • You will also need to install the appropriate MCR Installer for this Matlab executable file (more info at Source Forge)

    • For tomography data:

      • We recommend TomoPyUI for automated alignement and tomography reconstruction.

      • You will need AvizoTM or Dragonfly ORS or another 3D visualization capability for visualization of reconstructed tomography

Publication of Scientific Results

Please inform SSRL staff of all your publications from SSRL beam time. Publication within a reasonable period is expected for continued access to beam lines. Acknowledge the use of SSRL in your publication with the phrase "Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-76SF00515."