Prepare for a beamtime at TOMCAT

The following paragraphs summarize some important information to help you prepare for your beamtime at the TOMCAT beamline. Preparing your beamtime well in advance and paying attention to potentially critical or time-sensitive procedures helps us to ensure that your stay at TOMCAT will be as productive and efficient as possible.

A few formal procedures must be followed before arriving at PSI as a user. Please refer to the corresponding information on the PSI User Office website: Your stay at PSI

In particular, all people coming to PSI to take part in the experiments have to be registered as DUO users and need to request a badge and dosimeter for their visit through the DUO system at least a few days in advance. (They will need the accepted proposal number to schedule a visit to the TOMCAT beamline. This works even if they are not listed as co-proposers on the original proposal). Without a valid badge, the PSI site cannot be entered!

Each user experiment is supported by one of our local contacts, who will be your main point of contact, source of support and information before, during, and after your stay. You can find the name of your local contact in the DUO schedule for the TOMCAT beamline by choosing the appropriate month for your beamtime.

Further contact information of our staff is available on the staff website.

We kindly ask you to get in touch with your local contact well before the beginning of your beamtime in order to coordinate the beamtime preparations with her/him. Some equipment may need to be installed, reserved or calibrated before your arrival. Therefore, it is very important for us to know your exact requirements (which maybe not be described in detail in your proposal) well in advance of the scheduled beamtime.

Scheduled setup time

Setting up your experiment and cleaning up after your measurements is, in general, performed as part of the allocated beamtime. This may include setup changes from one technique or endstation to another, and integration of any custom sample environments in the beamline. Therefore, please plan for enough time at the beginning and the end of your measurements to help us assure a smooth changeover between users and to avoid delays for the next groups following your experiments.

Technical support

Our technical staff is usually available during normal office hours to help set up more involved experimental configurations with users. If you do require technical support, please notify your local contact well in advance.

Sample shape and size

The optimal sample shape for tomography is a cylinder. Try to prepare your samples as close as possible to such shape. An important parameter to be kept in mind during sample preparation is the sample absorption. Strong absorbing samples should be kept as small as possible.

Sample holders

It would be best if your samples would be mounted on pins, which fit our 3.15 mm sample holder. For precise specification, please consult: Sample holder specifications

Please do not hesitate to contact our beamline technicians (staff website), if you need more details.

Sample stability

To ensure highest data quality, samples must be stable throughout the entire measurement procedure. Even slight sample instabilities can significantly affect the reconstruction quality. Instability can arise from the reaction of the sample to the X-ray beam (bubble formation, desiccation, etc.), inappropriate sample preparation or fixation method, or from the choice of mounting materials. Consult with your local contact about the best way to prepare your samples to avoid motion artifacts, and possible strategies to minimize radiation-induced damage of your samples.

The TOMCAT beamline is optimized for high-resolution microtomography measurements, i.e., for samples measuring a few mm in width which can be measured at sub-micrometer resolution. Several microscopes with a rather wide range of different objectives (and consequently field of view and resolution) and different detectors are available (see our detectors page). Please note, however, that switching from one system to the other might need extra installation and calibration work at the beamline (up to 1 hour). This should be coordinated in advance with your local contact.

Onsite data storage policy

Your experimental data will be stored on our file server for a period of 60 days after your beamtime and will then be automatically removed. The main proposer will be notified of the data deletion two weeks in advance. Please plan and make sure to check and backup the collected data, immediately after returning to your institute. If you do find that some data is missing or incomplete, contact our staff immediately to retrieve the missing parts before deletion.

Backup policy

We would like to draw your attention to the fact that you are entirely responsible for the backup and security of your data. PSI and TOMCAT do not guarantee and cannot be made responsible for the safety of your experimental data against data loss. NO full BACKUP of your experimental data is done at PSI. However, PSI now offers long-term storage and retrieval capabilities, and within this context, we routinely archive a single (non-redundant) copy of all relevant raw data (only projections, no reconstructions) on the tape-based PetaByte archive system hosted at the Swiss National Supercomputing Center (CSCS) in Lugano, subject to the terms and conditions of the PSI Data Policy.

Typical data set sizes

Be aware that depending on the number of samples and scans, you might be producing very large amounts of data. Typical raw data sets for one scan are of the order of 15-20 GB (assuming 1500 - 2000 projections). Reconstructed data sets are approximately 14 GB for 8-bit tif files, 28 GB for 16 bit datasets and 56 GB for floating point number datasets (DMP format). Collecting 1-4 TB of data per day is rather normal. For dynamic studies with many time points, in excess of 30 TB per day can be generated.

Data transfer

Data is usually transferred by the users either via external hard drives or by network transfer. In any case, please check completeness of your data immediately upon returning to your home institution to allow for enough time to initiate a re-transfer in case of missing or incomplete data.

External hard drives

We strongly advise you to bring a sufficient number of empty (we are not responsible for lost data) external hard drives compatible with Linux (avoid disks especially formatted for Mac) for the data transfer and backup. WD Elements portable hard drives are particularly recommended, while we discourage the use of Seagate drives because of poor performance. USB3 or eSATA connections are a must for an efficient data transfer. Bringing your own network-attached storage (NAS) systems is also recommended if you are planning to acquire more than 6-10 TB of data.

Network transfer

Remote data transfer to your institution is also possible, but this service needs to be activated prior to your beamtime. If you are interested, please consult the Remote Transfer Information and contact your local support in advance.

If you need to import instrumentation or samples into Switzerland, please make sure to follow these import and shipping guidelines to guarantee proper Swiss custom clearance and avoid unnecessary costs or delays.

Please be aware that even samples imported personally by car/train/plane need to be properly declared, making use of the form to request authorization for carry-on samples. Before your trip to PSI, the document needs to be filled out, signed by you, and sent for validation to import@psi.ch. A validated and stamped copy will be promptly return to you. This document has then to be shown to customs when entering Switzerland. For any questions, do not hesitate to contact the PSI Import/Export Manager, Mr. Andre Teixeira (andre.teixeira@psi.ch, phone: +41 56 310 2913).

Make sure to allow sufficient time for shipments to arrive. Frequently, packages are held up by customs for inspection or further processing. This can cause significant delays of a few days or more, and may require intervention from our import/export office. Also note that PSI does not receive or distribute shipments on weekends.

PSI requires that you and your coworkers comply with all of the institute’s safety rules and regulations while working on the premises. You formally agreed to this by checking the relevant box while submitting your proposal online. It is the main proposer's responsibility to ensure that all team members who will work at the beamline have read and understood these safety regulations.

If anything regarding the safety aspects of your experiment changed with respect to what you declared at proposal submission, please let us know as soon as possible, so that the necessary safety assessment can be done prior to beamtime.

As a consequence of the increased acquisition speed over the past few years, beamtime at TOMCAT has become more demanding from the human resources point of view, even more so for complicated ultrafast in-situ and/or multi-days studies. To ensure successful experiments, efficient use of the time, and guarantee the safety of both people and equipment, we ask you to come to the beamline with sufficient staff to be able to work in shifts (and therefore get some sleep). We also strongly recommend to always work at least in pairs.

Failure to comply with the beamline safety advice and PSI regulations could lead to beamtime interruption: your local contact can and will STOP your experiment if during your beamtime safety issues are present or safety is at risk.

More information regarding safety at TOMCAT can be found on the safety page.