Beamtime at TOMCAT

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 beamlines. 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!

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. 

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

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. 

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.

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 beamlines 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 for your beamtime may need to be installed, reserved or calibrated before your arrival. 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.

Detector setup

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.

Setup and cleanup 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.

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 Office (import@psi.ch/export@psi.ch, phone: +41 56 310 34 10).

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.

Your main support and point of contact for all questions and issues during the beamtime is your local contact. To minimize the off-hour workload for your local contact, please plan work that requires assistance, like setup changes, during normal working hours. He or she is available from 07.00 until 23.00 during the week, using the numbers posted at the beamline and under the contact numbers on the website. On the weekend, user support is organized directly with the local contact.

Your local contact coordinates and organizes support from specialists, if required. However, please be aware that most support staff (technicians, infrastructure groups, IT experts, etc.) are not officially on call for beamtimes. Their help needs so to be scheduled during working hours. In case of failures and problems during the experiments, we will do our best to recover as quickly as possible to ensure that you can perform measurements efficiently, but delays can occur if support from specialists is required.

At the beginning of your experiment, your local contact will set up the experiments with you. This may require some setup changes in terms of hardware and software. Depending on the complexity of your experiments, and the state of the beamline at your arrival, this may take a few hours. We do our best to achieve optimal measurement conditions for all users, but quality takes time!

Once the beamline is ready for measurements, your local contact will instruct you step-by-step on how to run experiments at TOMCAT safely and independently. This includes a mandatory safety training and beamline orientation as well as information about:

• how to open and close the experimental hutch
• mounting and changing samples
• configuring and running the scans
• performing simple setup changes, if necessary
• reconstructing your data
• transferring your data onto your own storage device

It is very important that you follow these instructions carefully. Although your local contact is available for problems and questions throughout your beamtime, after a short training phase you are expected to run experiments independently. We recommend that your whole team is present and pays close attention during this instruction session, taking notes if necessary.

Data volumes at TOMCAT are high and the transfer process can be time-consuming. It is highly recommended to initiate the transfer and synchronization of your experimental data onto your storage devices or via network directly to your home institution as soon as the experiments are running and data is coming in. Your local contact will help you to set up the transfer. For more information, please refer to the Data Transfer section.

Beamtimes can be very intense and exhausting, in particular 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 and rest). We also strongly recommend to always work at least in pairs. If you nonetheless feel tired or your concentration is lapsing, please make sure to stop the experiment and have a rest to avoid accidents and costly mistakes. While we strive for an efficient use of beamtime at TOMCAT, we are committed to a safe working environment.

Disassembly of your experimental equipment and cleanup is considered part of your scheduled beamtime. Please make sure to plan enough time for it. The beamline is expected to be ready for handover to the next user group at the scheduled end time of your beamtime. 

Users are expected to help in keeping TOMCAT clean and well organized. Leave the beamline and TOMCAT areas in a similar state as you have found it or would like to find it. 

Additionally, please:

• Remove all samples and chemicals from the sample fridge and the sample preparation lab
• Remove all remaining food and drinks from the food fridge in the control room
• Clean up the sample preparation area and return all tools to their corresponding boxes
• Wipe the work surface in the sample preparation lab with standard alcohol (ethanol 70%)
• Do not pack and take away any items that belong to TOMCAT (usually labelled, but not always)
• Return any borrowed items to TOMCAT or the lender
• Don't forget any of your own items or equipment at TOMCAT
• Empty trash bins if they are getting full (a larger trash container can be found outside the beamline along the outside wall of SLS)
• Dispose of PET bottles and cardboard (Pizza) boxes in the corresponding recycling containers

If you have samples or materials that need to be disposed of at PSI, carefully instruct your local contact about what needs to be done and provide descriptions and labels for any items left at PSI (e.g.: disposal of chemicals, etc). 

It is acceptable to keep external hard drives connected to the corresponding media stations until transfer is complete. Make your local contact aware of it. Place a note on the computer notifying other people that file transfer is still in progress, and provide a contact address or phone number. If the transfer is not finish before you leave, hard drives can be send back to you at your cost. 

Thank you very much for your cooperation and help in maintaining a comfortable, efficient and safe work environment at TOMCAT!

Upon return to your home institution, please check carefully that you have a complete and intact copy of all your experimental data acquired at TOMCAT. As detailed in the data storage policy, your experimental data will be automatically deleted from the PSI servers after a retention period of 60 days (a reminder email will be sent to the main proposer two weeks prior deletion). In case you experience problems with the transfer or you do find that some data is missing or incomplete, notify your local contact immediately to retrieve the missing parts before deletion.

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.

Please note that shipping of hard drives or experimental equipment from SLS to your home institution will incur costs that are charged to you as the recipient. If you have any concerns, discuss any shipping issues with your local contact prior to your departure.

Also make sure to minimize the work load on your local contact and SLS staff by preparing the necessary shipping documents and packaging material ahead of time. Avoid shipment if possible.

To support users with their analysis needs, particularly when the data volume is important and a larger scale computing infrastructure is required, PSI has launched a local data analysis center that allows remote access for users to PSI infrastructure. Users can make use of a high performance computing cluster facility and a variety of installed software and tools. For example, the TOMCAT data reconstruction pipeline is installed on this cluster. Users can run their own reconstructions on PSI infrastructure from their home terminal. Users can also use their own specific custom tools for instance for data analysis and quantification directly on this facility.

More information about the data analysis center can be found here: Computing

Please take a few minutes to fill out and submit a brief end of run feedback form on your experiment and your stay at PSI. Your input is very valuable to us to improve and optimize our service at TOMCAT.

The feedback form can be found in the DUO system under
DUO > Proposals > Experiment feedbacks

or accessed directly under this link to the feedback forms in DUO.

Each experiment requires a short experimental report. This helps PSI track the progress and quality of experiments carried out here. In addition, the experimental reports are a very important input when submitting a new proposal. A missing report from a previous beamtime could potentially have a negative impact on the evaluation of the next one.

Guidelines to prepare the report:

• The experimental report should be submitted a few months after finishing an experiment
• The report should be 1-2 pages in length and contain some figures, if appropriate
• The report should contain a brief overview of the project, an evaluation of the quality of the measurements and data obtained from TOMCAT, a brief status report on the progress of analysis and evaluation, and some preliminary results.
• If a new proposal refers to a previous one, it is mandatory that the experimental report of the preceding experiment has already been submitted.
• The reports are treated confidentially and are only visible to beamline staff and the proposal review committee.

For more information, consult the SLS Guidelines on experimental reports.

The report has to be submitted via the DUO system under
DUO > Proposals > Experimental reports

You can also directly access the list of experimental reports in DUO.

For more information, refer to the SLS Publication Guidelines page.

All publications that include results based on data obtained at SLS should be registered in the DORA-PSI system. The number of papers and paper citations is taken as a measure of the impact of the SLS and of TOMCAT, which will influence the future financial support the facility and the beamline receive.

Please register your publication directly in DORA-PSI using this link. Please follow the link "Add Publication" from the DORA main menu.

DORA-PSI also serves as green open access repository for publications based on data taken at the PSI facilities to meet the recent guidelines for most funding agencies. For that purpose please also attach the "accepted versions" of your publications to the DORA-PSI database.

In addition to registering the publications in the system, please also notify your local contact or TOMCAT management of any published work.