--- language: "en" --- # BioXAS-Imaging * ## [About](https://bioxas-imaging.lightsource.ca/bioxas-imaging/about.md) * [Macro-mode](https://bioxas-imaging.lightsource.ca/bioxas-imaging/macro-mode.md) * [Micro-mode](https://bioxas-imaging.lightsource.ca/bioxas-imaging/micro-mode.md) * ### [User Guide](https://bioxas-imaging.lightsource.ca/bioxas-imaging/user-guide.md) * [New User](https://bioxas-imaging.lightsource.ca/bioxas-imaging/new-user.md) * [Proposal](https://bioxas-imaging.lightsource.ca/bioxas-imaging/proposal.md) * [Sample](https://bioxas-imaging.lightsource.ca/bioxas-imaging/sample.md) * [Beamtime](https://bioxas-imaging.lightsource.ca/bioxas-imaging/beamtime.md) * ### [FAQs and Data Transfer](https://bioxas-imaging.lightsource.ca/bioxas-imaging/faqs-and-data-transfer.md) * [FAQs](https://bioxas-imaging.lightsource.ca/bioxas-imaging/faqs.md) * [Remote Access](https://bioxas-imaging.lightsource.ca/bioxas-imaging/remote-access.md) * [Data Export](https://bioxas-imaging.lightsource.ca/bioxas-imaging/data-export.md) --- language: "en" --- # About ## Beamline layout The source of BioXAS Imaging beamline is an in-vacuum undulator producing a high spectral brilliance. The overall design of the beamline consists of a collimating mirror, a fixed-exit double crystal monochromator (DCM), a post-monochromator focusing mirror and the Kirkpatrick-Baez (KB) mirrors for micro-focusing the beam (micro mode). ![image-20260416-043225.png](https://bioxas-imaging.lightsource.ca/__attachments/a_7ca61189480af18ef8b505d00bedc9c32e540196869686e33b2e73058f4c904c/image-20260416-043225.png?cb=83270b3abc82c54df872c4020399bb32) Two insertion devices, undulator and wiggler, in the BioXAS straight. ![image-20250711-213308.png](https://bioxas-imaging.lightsource.ca/__attachments/a_735a44ccd66beed985f3140b9f206dfda0111331392c3e9634be102d1e1dc6a1/image-20250711-213308.png?cb=0c52cceab320f42469265d7b76efeab2) Schematic of BioXAS Primary Optics Enclosure. *** ** * ** *** ![Picture1-20260416-194953.png](https://bioxas-imaging.lightsource.ca/__attachments/a_0a862e9d16c90be4049646d0109ea9a97378c56f23718c24a321a3f442095bbb/Picture1-20260416-194953.png?cb=507c4c628051240974f5af50881a86c0) Schematic of the setup at the BioXAS Imaging beamline endstation. *** ** * ** *** ![_M8A2241.jpg](https://bioxas-imaging.lightsource.ca/__attachments/a_89f494051cd9d1acf40edc81da6791bd2c816b17d105fb666b4b3d61b20c4093/_M8A2241.jpg) BioXAS Imaging beamline endstation *** ** * ** *** ### **Source** * In-Vacuum Undulator (IVU) (Bruker ASC) * Minimum Gap: 5.2 mm * Maximum Gap: 40 mm * Total Number of Poles: 164 * Period: 19.1 mm * Total Length of Magnet Assemblies: 1600 mm * Peak field: 1.011 T ### **Beam** * Minimum Energy: 6 keV * Maximum Energy: 21 keV ### **Optics** * Pre-mono cyllindrical collimating mirror (M1): Si substrate with two reflective coatings (Si and Rh) * Post-mono toroidal focusing mirror (M2): Si substrate with Rh coating * KB mirrors: Si substrate with Rh coating *** ** * ** *** ### **Monochromator** * LN2-cooled constant exit height design (Kohzu) * Si(111) * Si (220), phi=0 deg ## **Detectors** * one 4-element Silicon Drift X-ray detector (Vortex-ME4, SII NanoTechnology) * one 3-element Silicon Drift X-ray detector (Vortex-ME3) * two single element Silicon Drift X-ray detectors (Vortex-EM, SII NanoTechnology) ## **Signal processing** * Xspress3 ([Quantum Detectors](http://quantumdetectors.com/)) --- language: "en" --- # Beamtime ## Important Notes * Users must let the beamline staff know in case there is a risk that the scheduled beamtime will not be utilized. There could be so many potential reasons for cancelation, to name a few, for example, the risk that the visa is not granted on time; the lab experiment required for the synchrotron experiment is not finished before the beamtime. * It is very important to be in communication with the beamline staff, in case of such a risk, because if alternatives are not possible to resolve the situation then the staff can tentatively schedule another project to utilize the canceled beamtime. ## Coming to CLS * In case you need accommodation during beamtime there are many hotels located in Saskatoon downtown or in proximity to the University of Saskatchewan. * For more information visit [Canadian Light Source](https://www.lightsource.ca/users/your-cls-experiment/before-your-beamtime.php#Plan%20Your%20Experiment). ![image-20250711-225958.png](https://bioxas-imaging.lightsource.ca/__attachments/a_db9ff19b1beb07242c335b38d721622532674f9315b4a48149f9d403f08f8741/image-20250711-225958.png?cb=c91b025736f2f2de2dde8c31b40fcb30) ## Facility access and training * First, you need to register as a CLS user and in order to gain access to the facility there are a number of requirements that need to be fulfilled, follow the instructions listed on the[Canadian Light Source](https://www.lightsource.ca/users/your-cls-experiment/practical-information/facility-access-and-training.php) website. * It is recommended to complete the training modules online prior to arriving at CLS because it would save considerable time during check-in at the User Service Office. ## Samples and Equipment * All samples and equipment, which you are planning to bring to CLS, must be reviewed and listed on the proposal. * Samples that are not on the proposal will not be permitted at CLS. * Samples/equipment can be amended through the user-portal project page way in advance. ## Sample shipment * International users must ship their samples following the instructions below. * The sample list within the package must also contain the following essential information: To/From Names, Beamline: BioXAS-Imaging; Beamline staff contact information; Proposal permit number; Sample list with clear naming; Storage specifications; Sample handling instructions. * Ship your approved sample prior to your scheduled beamtime. * Users are responsible for the cost of transportation and customs clearance for shipments; C.O.D packages are not accepted. * Packages must be addressed to the permanent staff of the BioXAS-Imaging beamline. * To expedite outgoing shipments, you can make round-trip shipping arrangements from your home institution. Please advise Shipping and Receiving if you have made these arrangements. ### **Shipment Address** Viorica (Ibi) Bondici or Mangaljit Singh \, Project \ (Project numbers can be found in User Portal) Canadian Light Source Inc. 44 Innovation Boulevard Saskatoon, Saskatchewan Canada S7N 2V3, Phone: 306-657-3657, Email: [stores@lightsource.ca](mailto:stores@lightsource.ca) More details about Canada Customs, shipment labels, and packaging requirements can be found under [Shipping](https://www.lightsource.ca/users/your-cls-experiment/practical-information/shipping.php). ## Contact information of the shipping and receiving department * Open times: Monday to Friday 8 am- 4:30 pm (closed for breaks from 10-10:15 am, 12-12:30 pm, 3-3:15 pm). * Contact information: email [stores@lightsource.ca](mailto:stores@lightsource.ca) , phone 306-657-3657. ## Beamline Specific Orientation (BSO) * All the users, who are collecting data at the BioXAS-Imaging beamline, are required to attend onsite training specific to the beamline. * This training covers all the hazards at the beamline, provides instructions on how to act in case of an emergency and how to operate the beamline safely. * Beamline staff will provide the training usually before the beamtime starts. **NOTE:** Physical modification to beamline components/setup should never be conducted without explicit approval or assistance from the beamline staff. ## User area * There are two computers available at the beamline, the linux operating system is used to operate the beamline and collect the data and the windows computer is utilized to communicate with various cameras for beamline diagnostic and monitoring. ## After Beamtime ### [Data Transfer](https://bioxas-imaging.lightsource.ca/bioxas-imaging/data-export) * The collected data are shared with the user through the [Globus platform](https://bioxas-imaging.lightsource.ca/bioxas-imaging/data-export). ### Sample/equipment * All your samples must be removed or you can arrange storage with beamline staff. * For information about shipping of samples/equipment from CLS please visit [Canadian Light Source Shipping](https://www.lightsource.ca/shipping.html). ### Housekeeping * Users are required to keep the area clean and tidy during their time at the beamline and clean up after themselves once beamtime is completed. --- language: "en" --- # BioXAS-Imaging Home ## Status: 🟢 Operational ![POE BioXAS.png](https://bioxas-imaging.lightsource.ca/__attachments/a_aa7b7c1fe0c7a7c3cf288d521bcda6c57e4f6b172ddfaa2d3e377f43496efb9b/POE%20BioXAS.png?cb=f80d7761c568fe7af47ee400a95bfe41) BioXAS Primary Optics Enclosure ## **BioXAS Sector** **BioXAS** isa newly commissioned beamline sector at the Canadian Light Source, comprising of three beamlines. The wiggler beamlines, BioXAS-Main and BioXAS-Side, are dedicated to X-ray Absorption Spectroscopy (XAS). The third, undulator beamline, BioXAS-Imaging, is a multi-resolution X-ray Fluorescence Imaging beamline. The BioXAS insertion devices occupy the same straight section of the storage ring but in a chicaned configuration to allow the beamlines to be operated independently. The **BioXAS-Imaging** beamline is a hard X-ray fluorescence imaging beamline with two spatial resolution modes currently in operation. The beamline has a spectral energy range between 5 to 21 keV. ![new_Spectral Range CLS beamlines.png](https://bioxas-imaging.lightsource.ca/__attachments/a_cc72ea24617f8ae25742d9ad7bc208b8d4a50e176da2676ca4de9898a3d7d1be/new_Spectral%20Range%20CLS%20beamlines.png?cb=0da0f5b61c9c4dabffeb21b031e5b90b) ![Start_page2.width-800.png](https://bioxas-imaging.lightsource.ca/__attachments/a_65417c43cefc04c22608d95b5f8c0f95a7c044896567f1ed3249b7bf28541afb/Start_page2.width-800.png?cb=3dd60ae3cf2d3669508355c0356b269a) ### **Disciplines** * Biological Science * Environmental Science * Cultural Heritage ### **Examples of research areas** * Bio-distribution of essential/toxic elements * Metals in various brain diseases * Metal-based compounds * Metals interaction with organisms in the environment * Accumulation, biotransformation, bioremediation ### **Techniques** * X-ray fluorescence imaging (XFI) * X-ray absorption spectroscopy imaging (XAS Imaging) * X-ray absorption spectroscopy experiments *in situ* (μ-XAS) ## **Quicklinks \>\>** * [CLS Website](http://www.lightsource.ca/) * [Storage Ring Status](http://mstatus.lightsource.ca/) * [CLS User Portal](https://user.lightsource.ca/) * [CLS Training Portal](http://training.lightsource.ca/) * [Grad Student Travel Support](https://www.lightsource.ca/users/your-cls-experiment/practical-information/travel-support-program.php) * [Acknowledging the CLS](https://www.lightsource.ca/users/your-cls-experiment/after-your-beamtime.php#AcknowledgingtheCLS) ### Latest Publications |-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| | Black, Tallan; Boseley, Rhiannon E.; Quirk, Amanda; Young, Kaylen M.; Lunardi-Baccetto, Sarah et al. (2026). *Adult Rat Offspring Exposed to THC during Gestation Exhibit Distinct Biomolecular Changes Identified by X-ray Fluorescence Imaging and Fourier Transform Infrared Spectroscopy in Cortico-Limbic Circuits* . ACS Chemical Neuroscience . [10.1021/acschemneuro.5c00752](https://dx.doi.org/10.1021/acschemneuro.5c00752). | | Deng, Ganqi; Vu, Miranda; Korbas, Malgorzata; Bondici, Viorica F.; Karunakaran, Chithra et al. (2025). *The study of the variation of mineral distribution and relative concentration on varieties of oat using synchrotron-based X-ray fluorescence imaging* . Food Research International 221, 117546. [10.1016/j.foodres.2025.117546](https://dx.doi.org/10.1016/j.foodres.2025.117546). | | Tunc, Ayetullah; Çelik, Yakup; Fociro, Ana; Deevsalar, Reza; Wang, Xinyi et al. (2025). *Distribution and speciation of uranium in pristine Tethyan phosphorites, Ionian Zone, Albania: Insights from synchrotron XRF/XANES analyses* . Journal of Geochemical Exploration 277, 107808. [10.1016/j.gexplo.2025.107808](https://dx.doi.org/10.1016/j.gexplo.2025.107808). | --- language: "en" --- # Data Export The data collected at the beamline first needs to be exported to the Globus cloud platform before transferring it to the local computer. This involves connecting remotely to the computer (if you are not on-site) and loggin into the PyAcq software to retrieve your data. The instructions can be found in the file here: [BioXAS Imaging Beamline Data Export Guide.pdf](https://bioxas-imaging.lightsource.ca/__attachments/a_52c0c624bd7191858935d3a669f7cae59ed47c16887ac4392cee49b97e234896/BioXAS%2520Imaging%2520Beamline%2520Data%2520Export%2520Guide.pdf.md?cb=4f2767736d4f290387fb442a46c8ed0f) Log out of your PyAcq session once the data export has been initiated. The export process will continue running in the background. The exported data contains multiple channels corresponding to different detectors. The data from all the channels shall be exported. Refer to the [setup schematic](https://bioxas-imaging.lightsource.ca/bioxas-imaging/about.md) to identify the detector positions and select the appropriate data channels for your analysis in Athena, Larch, PyMCA or any other software of your choice. For macro-mode experiments, use I1_dc_corr/scalar_1 (after_float) for data normalization. For micro-mode experiments, use I2_dc_corr/scalar_2 (after_float). In both cases, the selected signal is from the ion chamber located immediately upstream of the sample. ![detectors.png](https://bioxas-imaging.lightsource.ca/__attachments/a_bcad6dad59a0d556e7f3f46a8db68612bc3da5de97b344e6e84f65e903a63772/detectors.png?cb=0a737d493fc287bf9b7a2a6c5d828fdf) **dc_corr** and **dtc**imply dark-current corrected and dead-time corrected, respectively The exported data is then accessible on Globus platform and is attached to your *Canadian Light Source account and projects*. To retrieve the data, please follow this step-by-step guide. ## Acess CLS Data on Globus Globus delivers advanced file transfer and sharing capabilities to researchers no matter where their data live. [Globus](https://www.globus.org/) Connect Server makes it easy to add your lab cluster, campus research computing system, or other multiuser HPC facility to the Globus ecosystem. The CLS provides a Globus Connect Server endpoint that connects to our beamline data share, allowing users associated with scientific proposals access to their data. ## Step-by-Step Guide ### Log in * Access [**Globus**](http://app.globus.org/). * Select the **Canadian Light Source** as your institution. Click **Continue**. You will receive the familiar CLS sign-in page. ![image-20260429-164734.png](https://bioxas-imaging.lightsource.ca/__attachments/a_e705215c996038add002667fb1c54b483a9c38d929b58f4ea725c7461ab35b09/image-20260429-164734.png?cb=5cbecc7ec4fbc4a6bc434253fb064a5f) * Enter your **CLS username and password**. Your first log-in will register you with Globus' systems, which is important if other users want to share with you. ![image-20260429-164747.png](https://bioxas-imaging.lightsource.ca/__attachments/a_1ee6c352705ea6ec5284d687c75ca6b6973d5d9ff19743ecb5108d35e7385d3f/image-20260429-164747.png?cb=d64df44e7121f88558c03819bf5f5683) * Authentication/Consent authorization may be required upon the first login. Click **Continue** to proceed. ### File Manager \| CLS Beamline Data * Go to the **File Manager** view and select "SEARCH" * Search for the "**CLS Beamline Data**" Collection - this is our CLS endpoint on Globus ![image-20260413-162124.png](https://bioxas-imaging.lightsource.ca/__attachments/a_cf25b7a0540bf475e9e76ee01f6c67232127be42d3f9269d755818174523c17b/image-20260413-162124.png?cb=846501d603e12efe8e5c9ff34de27a0e) ### Path to Project Data * The **CLS Beamline Data** Collection will open with your CLS username as the Path and display any project folders you are involved in. * You will see the project you are interested in transfering data from. ### Set-up Personal Endpoint * In order to transfer the data to your personal computer, institution workstation or computing system you must first setup a personal endpoint. Your institution/you may already have this configured. If not: * Navigate to [Globus Connect Personal](https://www.globus.org/globus-connect-personal) * Install the Globus Connect Personal for your operating system * Launch Globus Connect Personal and 'Log In' to authenticate with Globus and begin the Collection Setup process. * Enter Collection Details for your Personal Setup and 'Save' ### Transfer Data from CLS to Your Endpoint * Select the files you wish to transfer to your computer An important note: Once you are on Globus, for a project number such as **prj123456** , and a username **user_abc,** please download files from the following directories: * **2D scan data:** /user_abc/prj123456/BIOXAS_IMAGING/export/hdf5/ * **XAS data:** /user_abc/prj123456/BIOXAS_IMAGING/export/xdi/ (**Note:** the "e" in **export** is lowercase.) * Select the desired destination * Click Start on CLS Beamline Data side. * The two-pane view works well for this. ![image-20260429-164814.png](https://bioxas-imaging.lightsource.ca/__attachments/a_110fc726e8d73bb0419c59833448ac708a9e46e81f0f031e39dc9185b8a65395/image-20260429-164814.png?cb=4a0c2286581e141426602731abd985cd) *** ** * ** *** ## Software and data analyses ### PyAcq software * Multi-threaded, Python-based data acquisition software with stand-alone GUI and Scanner, each can run independently. * Supports the following acquisition modes: one or two-positioner scan, fly scan imaging for macro-mode, step as well as fly scan imaging for micro-/nano-mode, with scaler signals and Xspress3-Vortex data. ### PyAcq powerful features * Dynamic ROIs view during data acquisition without delaying data update on the display. * Ability to view full MCA spectra from a single point or a defined region during data acquisition. ### Data analyses * Imaging data exported in HDF5 format compatible with [PyMca](http://pymca.sourceforge.net/) data analysis software. We recommend using **PyMCA version 5.9.1**. Newer versions may display errors when importing our HDF5 files. The recommended version can be downloaded here: [PyMca - Browse /pymca/PyMca5.9.1 at SourceForge.net](https://sourceforge.net/projects/pymca/files/pymca/PyMca5.9.1/) * XAS and μ-XAS data exported in XDI format compatible with [Athena](https://bruceravel.github.io/demeter/)/ [LARCH](https://xraypy.github.io/xraylarch/) softwares. ### PyMca software * The procedure on how to use the PyMca software for the BioXAS data analyses is shared with our users upon request. ### Larch software Detailed training videos on how to utilize the Larch software can be found [here](https://www.youtube.com/playlist?list=PLgNIl_xwV_vK4V6CmrsEsahNCAsjt8_Be). These videos present visualization and analysis of X-ray Absorption Spectra (XAS, XANES, and EXAFS) with the Larch XAS Viewer application. *** ** * ** *** ## We're here to help! ### If you encounter any issues, please let us know. [Contact us!](https://bioxas-imaging.lightsource.ca/bioxas-imaging/our-team) --- language: "en" --- # FAQs ## Frequently Asked Questions Some of the most common questions received from users: 1. Can I have my beamtime shifts rescheduled if I am not able to use my scheduled beamtime? No. In case, you are not using your beamtime due to an unanticipated reason, the awarded shifts will not be rescheduled. You will need to submit a BTR (Beamtime request) for the next cycle to re-schedule your beamtime. 2. If I lose beamtime due to technical problems related to operation issues, such as beam trip, will I get automatically those lost shifts? No. You will need to submit a BTR (Beamtime request) for the next cycle to re-schedule your beamtime. 3. Can I transfer my exported data onto an external hard drive? No external hard drives are allowed to be connected to beamline computers. Your data will be shared by beamline staff through [Globus data transfer](https://bioxas-imaging.scroll.site/bioxas-imaging/data-export) single interface system. --- language: "en" --- # FAQs and Data Transfer ## Frequently Asked Questions Some of the most common questions received from users: 1. Can I have my beamtime shifts rescheduled if I am not able to use my scheduled beamtime? No. In case, you are not using your beamtime due to an unanticipated reason, the awarded shifts will not be rescheduled. You will need to submit a BTR (Beamtime request) for the next cycle to re-schedule your beamtime. 2. If I lose beamtime due to technical problems related to operation issues, such as beam trip, will I get automatically those lost shifts? No. You will need to submit a BTR (Beamtime request) for the next cycle to re-schedule your beamtime. 3. Can I transfer my exported data onto an external hard drive? No external hard drives are allowed to be connected to beamline computers. Your data will be shared by beamline staff through [Globus data transfer](https://bioxas-imaging.lightsource.ca/bioxas-imaging/data-export) single interface system. ## Educational videos ## Useful readings [Localizing organomercury uptake and accumulation in zebrafish larvae at the tissue and cellular level](https://www.pnas.org/doi/10.1073/pnas.0803147105) [Elemental and chemically specific X-ray fluorescence imaging of biological systems](https://pubs.acs.org/doi/10.1021/cr4007297) [Synchrotron-Based X-Ray Fluorescence Microscopy as a Technique for Imaging of Elements in Plants](https://academic.oup.com/plphys/article/178/2/507/6116539) --- language: "en" --- # Macro-mode ## Status: 🟢 Operational The macro resolution mode is capable of rapid XRF imaging of relatively large samples. In addition, subregions of interest can be scanned with higher spatial resolution without changing the setup. A series of pinholes, which determines the beam size, are on a motorized stage and a beam size of interest (ranging between 20 to 150 μm) can be quickly selected during the same experiment. There are two stage-configuration available depending on the sample thickness. The 45 degrees stage-configuration with respect to the incident beam are generally set up for cross-sections varying from a few μm to a couple of hundreds of μm. For thicker samples with a thickness of mm range, the 90 degrees stage-configuration is used. ## Specifications * Four beam sizes are available between 20 and 150 μm defined by Pt or W apertures * Bi-directional fly scanning up to 20 ms dwell time * Two stage-configurations, 90 and 45 degrees, with respect to the incoming beam * Camera for scan setup/sample visualization * Samples under ambient air ## Flux The following fluxes are available with Pt aperture at 10 keV (5th harmonics). A similar flux can be obtained with the W aperture as well. * 20 μm: 0.6 x 10^11^ ph/s/100 mA * 50 μm: 3.5 x 10^11^ph/s/100 mA * 100 μm: 0.9 x 10^12^ph/s/100 mA * 150 μm: 1.4 x 10^12^ph/s/100 mA ![image-20260416-193558.png](https://bioxas-imaging.lightsource.ca/__attachments/a_a778e1b39f14dbd9a3172d3b16653a7937709b5326fe8bd0b6876adb4cf42e7a/image-20260416-193558.png?cb=37ad73974f8d14b8aff8c914dc5c5d9e) Distribution of K (green), Cu (blue), and Fe (red) in a Bumblebee. ## Setups The stage configuration can be changed depending on the thickness of the sample. ### **Stage configuration at 45 degree** ![image-20260416-200005.png](https://bioxas-imaging.lightsource.ca/__attachments/a_52dcbb48e1f72909dffac5c447a196fcb4958c2e9a86d23edc179d4d25abd03f/image-20260416-200005.png?cb=ad3fc0bc8624d21096d03b5aea621c92) The macro stage at 45 degrees orientation and the 4E Vortex detector at 90 degrees to the incident beam. This configuration is preferred for thin samples. ### **Stage configuration at 90 degree** ![image-20260812-193742.png](https://bioxas-imaging.lightsource.ca/__attachments/a_68e96a7d3abafbffefc623b6d73132d8fefd4e9bbc087dd9ce9563c2225495c5/image-20260812-193742.png?cb=18f97f74923601d0fcc9877e1ec06648) The macro stage at 90 degrees orientation and the 4E Vortex detector at 45 degrees to the incident beam. This configuration is preferred for thick samples to avoid shadowing effects in the data caused by the incident beam striking elevated features along its path if the beam is incident at 45°. --- language: "en" --- # Micro-mode ## Status: 🟢 Operational Designed for experiments that require greater/equal resolution to 10 μm. There are two stage-configuration available depending on the sample thickness. The 45 degrees stage-configuration with respect to the incident beam are generally set up for cross-sections varying from a few μms to a couple of hundreds of μms. For thicker samples reaching mm range, the 90 degrees stage-configuration is used. ![image-20260416-031139.png](https://bioxas-imaging.lightsource.ca/__attachments/a_bf503bd2f95f77eba0d61d34d589fea3df76fd5d1cf161ab16232869040ae149/image-20260416-031139.png?cb=8a775ada10b671d34221e04b648c5fd8) ## Specifications * Beam focused by KB mirrors * Step-based or bi-directional fly imaging * Sample stage at either 90 or 45 degress to the incoming beam * Keyence camera with long working distance (85 mm), high zoom (variable) lens for sample visualization * Samples in ambient air or He gas box * Cryo Jet/LN2 for sample cooling (to be commissioned) ## Beam size and flux Beam spot sizes measured at 45 degrees (meaning \~1.41X increase in beam H size) and at 10 keV (5th harmonics): * 10 μm (H) x 5 μm (V) flux 3.2 x 10^11^ ph/s/100 mA (full focused beam limited only by the acceptance of the KB mirrors) * 6 μm (H) x 5 μm (V) flux 1.5 x 10^11^ph/s/100 mA (beam cut horizontally at the secondary source) ## Techniques * X-ray fluorescence imaging (XFI) * X-ray absorption spectroscopy (XAS) * X-ray absorption spectroscopy in situ (u-XAS) ## Examples * Stage configuration at 45 degrees to the incident beam * The imaging data were collected at a resolution of 5 um at 100 ms dwell time ![image-20250711-213528.png](https://bioxas-imaging.lightsource.ca/__attachments/a_60b155adda049d6e2020ac9307561cf1600b70ec0fe619d98915b01f51d2a0d5/image-20250711-213528.png?cb=86ea848bae8a5a19d3ef0d76d73a09fe) Distribution of Micronutrients in Arborg Oat *(Avena sativa L.)* Using Synchrotron X-ray Fluorescence Imaging (Deng et al., 2023). *** ** * ** *** ## Setups The stage configuration can be changed depending on the thickness of the sample. ## Stage configuration set at 45 degrees ![image-20250711-213520.png](https://bioxas-imaging.lightsource.ca/__attachments/a_5701edee7515dc1fd3cf3f09e807f4fe24258855fba1ed3b5bb97417940b07fd/image-20250711-213520.png?cb=c26dd8b4bbb5b0bbbc6a7d0fa198de64) The micro stage at 45 degrees orientation and the 4E Vortex detector at 90 degrees to the incident beam. This configuration is preferred for thin samples. ## Stage configuration set at 90 degrees ![image-20250711-213540.png](https://bioxas-imaging.lightsource.ca/__attachments/a_430417fdadc53d2b84b115697b16fc40e95f70785cce4d82b6be4ed305eb2c43/image-20250711-213540.png?cb=3e0985c71c8ac7d98c6fc81a8bfd07bc) The micro stage at 90 degrees orientation and the 4E Vortex detector at 45 degrees to the incident beam. This configuration is preferred for thick samples to avoid shadowing effects in the data caused by the incident beam striking elevated features along its path if the beam is incident at 45°. --- language: "en" --- # New User ## How to get beamtime The Canadian Light Source [calls for Research Proposals](https://www.lightsource.ca/users/getting-started/applying-for-beamtime.php) twice per year and beamtimes are scheduled in 6-month cycles. ## **Beamtime can be accessed** * **Peer-Reviewed Access**- proposals are submitted during an open Call for Proposals which is a competitive peer review process and beamtime is granted based on scientific merit (Fee $1 per 8-hour shift). * **Rapid Access**- is a special request outside of the peer-review cycles. It is required that you contact the beamline responsible prior to submitting your proposal (Fee $1 per 8-hour shift). * **Purchased Access-** is through the [Industrial Science](https://www.lightsource.ca/industry/services/purchased-access.php) program with full-service synchrotron access with charge. ## Registration Detailed instructions on how to register and manage your account can be found under [User Portal Guide](https://www.lightsource.ca/users/getting-started/user-portal-guide.php#HowtoRegister). Important information regarding proposal and beamtime requirements are found in this portal. New users need to be aware and ensure that the User Agreement and Institutional Agreement are up to date. --- language: "en" --- # News NEWS ![PALSA-20250326-195603.png](https://bioxas-imaging.lightsource.ca/__attachments/a_096d2dc4f7f9997100251561dd56c3587c9d3e4d403d5871fe196da39f8ecfdd/PALSA-20250326-195603.png?cb=a7cbf51f05739d09c59080525ed16ae7) **Annual workshop: Register before May 15, 2025** March 24, 2025 2nd Annual CLS Introduction to X-ray Absorption Spectroscopy and Microprobe Workshop (August 18-19, 2025): Registration Now Open NEWS ![PALSA2025-20250324-185646.jpg](https://bioxas-imaging.lightsource.ca/__attachments/a_961444891c4e46cd60b317943b9c825e1d7410b13d9c69468b02cda3c2253cca/PALSA2025-20250324-185646.jpg?cb=638e8f928782fc16a5176db6dd5219f8) PALSA Conference: Register before June 15, 2025 March 24, 2025 The 4th International Pan American Light Sources for Agriculture (PALSA 2025) meeting is scheduled to take place from August 20 to 22, 2025, in Saskatoon, Saskatchewan. NEWS ![hiring_new-20260416-031505.png](https://bioxas-imaging.lightsource.ca/__attachments/a_f8c8a3905c017c4688af67bafe2553d70d5b381c878de325b8077b8810daf087/hiring_new-20260416-031505.png?cb=51d50664308a21a096aa8a53e4e100ca) [++BioXAS Sector is Hiring (Expired)++](https://bioxas-imaging.lightsource.ca/news/bioxas-sector-hiring/) July 26, 2024 Associate Scientist (BioXAS Imaging) - Canadian Light Source Inc. ([http://northstarats.com](http://northstarats.com/) ) *** ** * ** *** BEAMLINE UPDATES ![general_phase-20260416-031451.png](https://bioxas-imaging.lightsource.ca/__attachments/a_6b7cb1824f3ffd005356b11f960cc11df077431625d355ad4c4f2a69aaf6d555/general_phase-20260416-031451.png?cb=41600f8e9fe805245c84095c09e12d7d) BioXAS Imaging has recently entered General User phase Jan. 7, 2021 BioXAS Imaging Macro and Micro resolution modes have entered the General User phase and accepting proposals. RESEARCH HIGHLIGHTS ![oat_new-20260416-031542.png](https://bioxas-imaging.lightsource.ca/__attachments/a_f275575b4785a433f40cb8978ef27bb43f6455a5591c79379c2b213c1a86cefa/oat_new-20260416-031542.png?cb=5e197a51f419e36c8310d234b2cee121) Distribution of micronutrients in Aborg Oat (*Avena sativa L.* ) using synchrotron X-ray fluorescence imaging in micro-mode. BEAMLINE UPDATES ![image-20250711-233737.png](https://bioxas-imaging.lightsource.ca/__attachments/a_0aef7f9a1faa9f78cc6b4435777ffb795a70b87cc413e3ad80f05df1161de3a5/image-20250711-233737.png?cb=5bf0907a0a974f1aebc40610d7adace0) **FRONT END MASK REPLACEMENT** Aug. 4, 2021 The BioXAS sector was experiencing vacuum issues during the previous cycle. Front End mask was replaced during the spring shut-down. *** ** * ** *** RESEARCH HIGHLIGHTS ![mouse_new-20260416-031525.png](https://bioxas-imaging.lightsource.ca/__attachments/a_4b389165b3ec1909aa9aa973a119073fdaeede59bd2dfc0ef37db04c8390cf8a/mouse_new-20260416-031525.png?cb=1b421f3a2759eee629299cef9a7d2ba8) **XRF IMAGING OF WHOLE BODY MOUSE SECTION** March 31, 2021 Data of whole body mouse (model organism) section were collected in Macro-mode at 100 micron resolution and 60 ms dwell time. Beamline Updates ![image-20250711-233924.png](https://bioxas-imaging.lightsource.ca/__attachments/a_f8a731184874bdddd22754a0df3ae6d25240d9631e5f27fb3e6d094e6540fa38/image-20250711-233924.png?cb=269b61b9a759f6a811a269cf11d82516) **AIR CONDITIONING SYSTEM INSTALLED** Jan. 25, 2021 The installed air conditioning system will provide the optimum temperature in the enclosures aiding beam stability over time. Beamline Updates ![image-20260416-183907.png](https://bioxas-imaging.lightsource.ca/__attachments/a_409e95527aefaca22628bad91b581b34fa636e1d8d2ba058197c8db81854749c/image-20260416-183907.png?cb=c3528134e561e0b7dc1e6052722171aa) **FIRST USER AT THE BEAMLINE** Jan. 14, 2020 Our first BioXAS-Imaging user at the beamline collected data in micro-mode to investigate phytoremediation potential of plants grown at mining impacted site. *** ** * ** *** Beamline Updates ![xrf_micro.png](https://bioxas-imaging.lightsource.ca/__attachments/a_25b2c5d78a168e08583c3353251d913e92116325fa0f22dcfc9b7c6309bb3cd6/xrf_micro.png?cb=de18b5c3148c1388a5bf063c763437cb) **FIRST XRF IMAGES COLLECTED IN MICRO-MODE** Oct. 24, 2019 XRF images representing Ca, Zn, Hg and S distribution in zebrafish. Data were collected as fly scan in micro-mode at 5 μm resolution. News ![image-20260416-184503.png](https://bioxas-imaging.lightsource.ca/__attachments/a_7640fdc93d23697e06f59809ac6554c72ffce4bc9356ee56dd9b9f40cd24dabd/image-20260416-184503.png?cb=0274b47f53075e84cc136d3fe3163d27) **STUDENTS AT THE BEAMLINE** June 2, 2019 Copper uptake in brown algae was studied using fly scan XRF imaging in Macro-mode at 100 μm resolution and 50 ms. Beamline Updates ![xrf_macro.png](https://bioxas-imaging.lightsource.ca/__attachments/a_4d919452885a7b22325483607e4b77fe7abe518c1b766a6b962bb87d24caf5e4/xrf_macro.png?cb=26f60efcc340b79b6da7f018faa9aa23) **XRF IMAGES COLLECTED IN MACRO-MODE** Feb. 15, 2019 Distribution of Mn and Zn in dry leaves collected in macro-mode at 20, 50 and 150 um resolutions. *** ** * ** *** Beamline Updates ![image-20260416-185008.png](https://bioxas-imaging.lightsource.ca/__attachments/a_7f3d8ec5a6319355748f6a074e51fde720ab1b9f966d2678f961d2ae5231ed64/image-20260416-185008.png?cb=648b28806ab49ea12ce6416133980092) **FIRST XRF IMAGE COLLECTED IN MACRO-MODE** June 9, 2017 Although dry leaves could depict an end, but for us, this image meant a beginning, a start to contribute to science and knowledge. --- language: "en" --- # Our Team | ![2.jpg](https://bioxas-imaging.lightsource.ca/__attachments/a_91513522d34c8d069a9bfa2d41e5fcbaa2261f23c377499c5adf4cebbc8d70e2/2.jpg?cb=fc360def764e1071055833ee33a01a0e) | **[**Viorica (Ibi) Bondici**](mailto:Ibi.Bondici@lightsource.ca)** **Scientist (BioXAS-Imaging)** [**ibi.bondici@lightsource.ca**](mailto:ibi.bondici@lightsource.ca) **2069** **(306) 657-3707** | | ![7B178CD0-8261-4F70-8E34-E2173A4BCBDA2026-01-29_13-32-29_824 - Copy (2).jpeg](https://bioxas-imaging.lightsource.ca/__attachments/a_5996116d6a717a86cf64aaa0b7601048d0e72639fe8a82cdd086c6dc95dbece0/7B178CD0-8261-4F70-8E34-E2173A4BCBDA2026-01-29_13-32-29_824%20-%20Copy%20(2).jpeg?cb=d4eba0d9303fc730ab564d7aac8eeffc) | **[**Mangaljit Singh**](mailto:mangaljit.singh@lightsource.ca)** **Associate Scientist (BioXAS-Imaging)** [**mangaljit.singh@lightsource.ca**](mailto:mangaljit.singh@lightsource.ca) **2069** **(306) 657-3584** | | ![image-20260416-024914.png](https://bioxas-imaging.lightsource.ca/__attachments/a_1e3dcb75725654fa6a1e926b2f016bf307e80d6390beaec1947d734906bf3a56/image-20260416-024914.png?cb=bbd4e263e8c1328bb1be9dab71f8d54b) | **[**Amanda Quirk**](mailto:Amanda.Quirk@LIGHTSOURCE.CA)** **Scientist, Bio/Life Science and Mid-IR** [**amanda.quirk@lightsource.ca**](mailto:amanda.quirk@lightsource.ca) **2074** **(306) 657-3755** | | ![1687972059945.jpeg](https://bioxas-imaging.lightsource.ca/__attachments/a_76ae1102bed824e7e4568069c18a98e1be8d355394989b267b33ffbf416a1d54/1687972059945.jpeg?cb=d1f813a8f9dab5a29e235a69caedc811) | **[**Ozra Mohammadi**](mailto:Ozra.Mohammadi@lightsource.ca)** **Associate Scientist (BioXAS-Spectroscopy/Imaging)** [**ozra.mohammadi@lightsource.ca**](mailto:ozra.mohammadi@lightsource.ca) **2067** **(306) 657-3694** | | ![image-20260416-042049.png](https://bioxas-imaging.lightsource.ca/__attachments/a_173d19a79af8186d976532bb7891a8cf04ceade2b93182888299a85e087beead/image-20260416-042049.png?cb=ac0ef7686484bef52b4bb687c268035c) | **[**Zachary Arthur**](mailto:Zachary.Arthur@lightsource.ca)** **Scientist - BioXAS Sector Responsible** [**zachary.arthur@lightsource.ca**](mailto:zachary.arthur@lightsource.ca) **2070** **(306) 657-3708** | |-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| ## Phone Numbers * 07ID-1 beamline: **306-657-3625** * Reception: **306-657-3500** * Fax number: **306-657-3535** ## Local Emergency Contacts * The Floor Coordinator: ext. **3639** * Emergency: **9-911** * University of Saskatchewan Security: **9-306-966-5555** * CLSI HSE 24/7 On-call: **9-306-227-3113** * CLSI HSE Normal Business Hours: ext. **3663** ### [++**CLS Contacts and Staff Directory**++](https://www.lightsource.ca/about/contact.php) ## Mailing Address Canadian Light Source Inc. University of Saskatchewan, 44 Innovation Boulevard 44 Innovation Boulevard Saskatoon, SK, Canada S7N 2V3 ## BioXAS beam-team leader ![image-20260617-042944.png](https://bioxas-imaging.lightsource.ca/__attachments/a_10a9c31324577e97d8d2eb1fb04d6b3e5d523745571cd5b2d1f6966c2617b323/image-20260617-042944.png?cb=49eb6a13fd9f1774e1c003b4dd7da056) [Joyce McBeth](https://www.uregina.ca/science/earth-sciences/directory/faculty/joyce-mcbeth.html), Assistant Professor, University of Regina, Canada ## Former Senior Scientist/Beamline Sector Responsible ![image-20260617-043005.png](https://bioxas-imaging.lightsource.ca/__attachments/a_26e6bf93a85e35cde004555c33012eecde23e845e59e64548b279c31619f98db/image-20260617-043005.png?cb=8c9ab9a93eb74fdbe144288e3a744fda) [Gosia Korbas](https://www.anl.gov/profile/gosia-korbas), Beamline scientist -- Microscopy, Argonne National Laboratory, USA --- language: "en" --- # Proposal First, check when the next [call for proposals](https://www.lightsource.ca/users/getting-started/applying-for-beamtime.php) opens. Information and detailed instructions on how to create a new proposal for submission in the User Portal can be found under [How to submit a proposal.](https://www.lightsource.ca/users/getting-started/user-portal-guide.php#OntheDashboard) It is important to note that active proposals will not be automatically valid in the next cycle, users need to submit a Beam Time Request (BTR) when there is an open Call for Proposals. ## Important tips There are a few points that can be considered and incorporated into the corresponding sections for a successful proposal: * The research project needs to be novel with a well-defined scientific question that could only be answered with the technique(s) offered by the BioXAS-Imaging beamline. * Include information with the necessary description that your sample is compatible with this technique. * Provide sufficient explanation to justify how the utilization of this technique will benefit your research project. * Include any preliminary data from the beamline or complementary data from other imaging techniques to help the reviewer understand the objective of the project. * Justify the number of shifts required based on the number of samples that are essential to be able to answer your research question. * Since obtaining beamtime is very competitive knowing how many shits to request is important. Instruction on how to calculate the time required for an imaging scan can be found below. ## Time estimation for a scan ## Example 1. Let's assume you need to scan an area of 1 mm x 1 mm with a resolution of 10 um and 100 ms dwell time per pixel. Dwell time can be defined as how much time the beam spends on a pixel and can vary between experiments. Detection of elements with low abundance can be improved with longer dwell time. 2. Basically, you need to calculate how many pixels are in an area of interest and multiply that by the dwell time in seconds. 3. Then the time required for the scan (purely based on the parameters above) is (1 mm/0.01 mm) x (1 mm/0.01 mm) x 0.1 s = 100 x 100 x 0.1 s = 1000 s, so approximately 17 mins. 4. Please add 10% to it as the stages need time to move up to a new horizontal line. 5. Thus, the total time in the proposal for such an image would be 17 mins + 10% x 17 mins = 19 mins ## Proposal amendments It is the responsibility of the User to ensure that the BioXAS-Imaging beamline project proposal is up to date, particularly that the samples and standards intended for the experiment are on the list. Samples/Standards that are not on the list are not permitted and will not be allowed to be run on the BioXAS-Imaging beamline, therefore, in case of additional samples, the proposal needs to be updated accordingly. To receive Health, Safety, and Environment (HSE) approval on time, it is recommended to make the amendments to the submitted proposal at least 4 weeks before the scheduled beamtime. Also, ensure that all members of the User group, who plan to participate in the data collection, must be on the proposal. --- language: "en" --- # Publications | Cite | Date | |------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------| | Black, Tallan; Boseley, Rhiannon E.; Quirk, Amanda; Young, Kaylen M.; Lunardi-Baccetto, Sarah et al. (2026). *Adult Rat Offspring Exposed to THC during Gestation Exhibit Distinct Biomolecular Changes Identified by X-ray Fluorescence Imaging and Fourier Transform Infrared Spectroscopy in Cortico-Limbic Circuits* . ACS Chemical Neuroscience . [10.1021/acschemneuro.5c00752](https://dx.doi.org/10.1021/acschemneuro.5c00752). | 2026-02-09 | | Ashe, Paula; Tu, Kaiyang; Stobbs, Jarvis A.; Dynes, James J.; Vu, Miranda et al. (2025). *Applications of synchrotron light in seed research: an array of x-ray and infrared imaging methodologies* . Frontiers in Plant Science 15. [10.3389/fpls.2024.1395952](https://dx.doi.org/10.3389/fpls.2024.1395952). | 2025-02-17 | | Bangash, Sami Ullah; McNeill, Fiona E.; Farquharson, Michael J.; Wainman, Bruce; Zeller, Michelle et al. (2025). *Performance testing a portable 109Cd XRF system for the measurement of ex vivo skin iron content in a rat model of iron overload* . Nuclear Instruments and Methods in Physics Research. Section B: Beam Interactions with Materials and Atoms 563, 165696. [10.1016/j.nimb.2025.165696](https://dx.doi.org/10.1016/j.nimb.2025.165696). | 2025-06-01 | | Deng, Ganqi; Vu, Miranda; Korbas, Malgorzata; Bondici, Viorica F.; Karunakaran, Chithra et al. (2025). *The study of the variation of mineral distribution and relative concentration on varieties of oat using synchrotron-based X-ray fluorescence imaging* . Food Research International 221, 117546. [10.1016/j.foodres.2025.117546](https://dx.doi.org/10.1016/j.foodres.2025.117546). | 2025-12-01 | | Desmau, Morgane; Skierszkan, Elliott K.; Oka, Gladys; Kaur, Inderjeet; Schoepfer, Valerie A. et al. (2025). *Multi-contaminant removal from synthetic mine-impacted water by permeable reactive barriers under cold conditions* . Chemosphere 384, 144499. [10.1016/j.chemosphere.2025.144499](https://dx.doi.org/10.1016/j.chemosphere.2025.144499). | 2025-09-01 | | Indore, Navnath S.; Jayas, Digvir S.; Karunakaran, Chithra; Stobbs, Jarvis; Bondici, Viorica F. et al. (2025). *Application of synchrotron imaging techniques for study of changes in microstructural and nutritional properties of different wheat classes in storage* . Journal of Stored Products Research 111, 102576. [10.1016/j.jspr.2025.102576](https://dx.doi.org/10.1016/j.jspr.2025.102576). | 2025-05-01 | | Lee, Andre P. C.; Aziz, Fatima; Karimian Bahnamiri, Fazele; Korbas, Malgorzata; Bondici, Viorica F. et al. (2025). *Elucidating Cation Transport Properties in Nafion Membranes and Electrode Ionomer Network via X-ray Fluorescence Imaging* . Journal of the Electrochemical Society 172(6) , 064502. [10.1149/1945-7111/addd6a](https://dx.doi.org/10.1149/1945-7111/addd6a). | 2025-06-01 | | Santos, Eduardo; Montanha, Gabriel Sgarbiero; da Silva, Higor José Freita Alves; da Silva, Nicolas Gustavo da Cruz; Franco, Felipe Sousa et al. (2025). *Resolving the Foliar Calcium Mobility Paradox: Enhancing Foliar Calcium Transport in Tomato Using Osmotic Regulators* . Patent Number: [10.1101/2025.07.02.662739](https://patents.google.com/patent/10.1101/2025.07.02.662739/en). | 2025-07-02 | | Simpson, Rachel M. L. (2025). *Lead exposure in Corinth and Stymphalos, Greece, in late antiquity: A chemical investigation of archaeological skeletal remains* . Supervisor: Garvie-Lok, Sandra. Alberta, Canada: University of Alberta. . | 2025-11-03 | | Tchobanian, Armen; Kim, Damin; Pahara, Justin (2025). *3D X-ray fluorescence imaging of insect pests and analysis in a virtual reality environment* . Canadian Journal of Chemistry . [10.1139/cjc-2024-0246](https://dx.doi.org/10.1139/cjc-2024-0246). | 2025-07-08 | | Tunc, Ayetullah; Çelik, Yakup; Fociro, Ana; Deevsalar, Reza; Wang, Xinyi et al. (2025). *Distribution and speciation of uranium in pristine Tethyan phosphorites, Ionian Zone, Albania: Insights from synchrotron XRF/XANES analyses* . Journal of Geochemical Exploration 277, 107808. [10.1016/j.gexplo.2025.107808](https://dx.doi.org/10.1016/j.gexplo.2025.107808). | 2025-10-01 | | Wasiljeff, Joonas; Yu, Changxun; Heikkilä, Pasi; Lahaye, Yann; Kurhila, Matti et al. (2025). *Mineral phases and growth conditions of morphologically diverse shelfal ferromanganese concretions* . Geochimica et Cosmochimica Acta . [10.1016/j.gca.2025.05.012](https://dx.doi.org/10.1016/j.gca.2025.05.012). | 2025-05-01 | | Almazan, E.R.; Affolder, A.; Dyckes, I.; Fadeyev, V.; Hance, M. et al. (2024). *Characterizing novel Indium Phosphide pad detectors with focused X-ray beams and laboratory tests* . Journal of Instrumentation 19(11) , P11016. [10.1088/1748-0221/19/11/p11016](https://dx.doi.org/10.1088/1748-0221/19/11/p11016). | 2024-11-01 | | Bangash, Sami Ullah; McNeill, Fiona E; Farquharson, Michael J (2024). *Investigation of the accuracy of a portable ^109^Cd XRF system for the measurement of iron in skin* . Biomedical Physics and Engineering Express 10(3) , 035032. [10.1088/2057-1976/ad3d60](https://dx.doi.org/10.1088/2057-1976/ad3d60). | 2024-04-22 | | Budimir, Filip; Ptacek, Carol J.; Amos, Richard T.; Blowes, David W. (2024). *Chromium isotope fractionation during the removal of hexavalent chromium by oak-based biochar* . Chemosphere 369, 143880. [10.1016/j.chemosphere.2024.143880](https://dx.doi.org/10.1016/j.chemosphere.2024.143880). | 2024-12-01 | | Nakhforoosh, Alireza; Hallin, Emil; Karunakaran, Chithra; Korbas, Malgorzata; Stobbs, Jarvis et al. (2024). *Visualization and Quantitative Evaluation of Functional Structures of Soybean Root Nodules via Synchrotron X-ray Imaging* . Plant Phenomics 6, 0203. [10.34133/plantphenomics.0203](https://dx.doi.org/10.34133/plantphenomics.0203). | 2024-07-17 | | Pushie, M Jake; Sylvain, Nicole J; Hou, Huishu; Pendleton, Nicole; Wang, Richard et al. (2024). *X-ray fluorescence mapping of brain tissue reveals the profound extent of trace element dysregulation in stroke pathophysiology* . Metallomics . [10.1093/mtomcs/mfae054](https://dx.doi.org/10.1093/mtomcs/mfae054). | 2024-11-15 | | Skierszkan, Elliott K.; Schoepfer, Valerie A.; Fellwock, Matthew D.; Dockrey, John W.; Hayatifar, Ardalan et al. (2024). *Arsenic Mobilization from Thawing Permafrost* . ACS Earth and Space Chemistry 8(4) , 745-759. [10.1021/acsearthspacechem.3c00355](https://dx.doi.org/10.1021/acsearthspacechem.3c00355). | 2024-03-19 | | Skierszkan, Elliott K.; Schoepfer, Valerie A.; Fellwock, Matthew; Lindsay, Matthew B. J. (2024). *Uranium Speciation and Mobilization in Thawing Permafrost* . Environmental Science and Technology . [10.1021/acs.est.4c05594](https://dx.doi.org/10.1021/acs.est.4c05594). | 2024-09-13 | | Deng, Ganqi; Vu, Miranda; Korbas, Malgorzata; Bondici, Viorica F.; Karunakaran, Chithra et al. (2023). *Distribution of Micronutrients in Arborg Oat (Avena sativa L.) Using Synchrotron X-ray Fluorescence Imaging* . Food Chemistry , 135661. [10.1016/j.foodchem.2023.135661](https://dx.doi.org/10.1016/j.foodchem.2023.135661). | 2023-02-01 | | Indore, Navnath S.; Jayas, Digvir S.; Karunakaran, Chithra; Stobbs, Jarvis; Bondici, Viorica F. et al. (2023). *Study of Microstructural, Nutritional, and Biochemical Changes in Hulled and Hulless Barley during Storage Using X-ray and Infrared Techniques* . Foods 12(21) , 3935. [10.3390/foods12213935](https://dx.doi.org/10.3390/foods12213935). | 2023-10-27 | | Indore, Navnath S.; Karunakaran, Chithra; Jayas, Digvir S.; Bondici, Viorica F.; Vu, Miranda et al. (2023). *Mapping biochemical and nutritional changes in durum wheat due to spoilage during storage* . Heliyon 9(11) , e22139. [10.1016/j.heliyon.2023.e22139](https://dx.doi.org/10.1016/j.heliyon.2023.e22139). | 2023-11-01 | | Milla-Moreno, Estefanía (2023). *An assessment of native Chilean woody plants for phytoremediation of copper-contaminated sites* . Supervisor: Guy, Robert D.. British Columbia, Canada: University of British Columbia. . | 2023-04-19 | | Uwanyirigira, Janviere (2023). *Integrated Synchrotron Approaches to Characterize Organic Matter-Iron Phases Relevant to Passive Mine Waste Remediation Systems* . Supervisor: McBeth, Joyce. Saskatchewan, Canada: University of Saskatchewan. . | 2023-07-25 | | Milla-Moreno, Estefanía; Guy, Robert Dean; Soolanayakanahally, Raju Y. (2022). *Enlightening the Pathway of Phytoremediation: Ecophysiology and X-ray Fluorescence Visualization of Two Chilean Hardwoods Exposed to Excess Copper* . Toxics 10(5) , 237. [10.3390/toxics10050237](https://dx.doi.org/10.3390/toxics10050237). | 2022-05-06 | | Scott, Sarah Barbara (2022). *The impacts of common urban metals on Bombus impatiens colony health and behavior* . Supervisor: Gardiner, Mary. Ohio, USA: Ohio State University. . | 2022-11-29 | | Grochulski; P.; Fodje; M.N.; George et al. (2012). *Status and Vision for Structural Biology at the Canadian Light Source* . In Acta Physica Polonica A. Institute of Physics, Polish Academy of Sciences, Poland. , 866-870 [10.12693/APhysPolA.121.866](https://dx.doi.org/10.12693/APhysPolA.121.866). | 2012-01-01 | AUTO_PUBLISH_1785253687085 AUTO_PUBLISH_1785352328220 AUTO_PUBLISH_1785354927632 AUTO_PUBLISH_1785357480100 AUTO_PUBLISH_1785869924845 AUTO_PUBLISH_1785954885447 AUTO_PUBLISH_1786462946771 AUTO_PUBLISH_1786476747988 AUTO_PUBLISH_1786477423349 AUTO_PUBLISH_1787616011254 AUTO_PUBLISH_1787702410409 AUTO_PUBLISH_1787788809899 AUTO_PUBLISH_1787875210344 AUTO_PUBLISH_1787961609862 AUTO_PUBLISH_1788048009710 AUTO_PUBLISH_1788134409869 AUTO_PUBLISH_1788220810096 AUTO_PUBLISH_1788307210617 AUTO_PUBLISH_1788393609386 AUTO_PUBLISH_1788480006375 AUTO_PUBLISH_1788566407966 --- language: "en" --- # Remote Access ## Remote Access to the BioXAS Beamline Workstations Remote access to the beamline computers is provided through the NoMachine server. ### Install NoMachine Enterprise Client: Before beam time please download and install NoMachine: * On your PC, navigate to: * Follow the download instructions for the NoMachine Enterprise Client appropriate to your computer and operating system * Install the Client onto your computer ### Setup your connection: * Start NoMachine Enterprise Client * Select Add under machines → Add connection ![image-20260429-162945.png](https://bioxas-imaging.lightsource.ca/__attachments/a_fbb07b2a955ad657c38b987d4285d700dec712e90d490f34d5ef214fa4bef4e9/image-20260429-162945.png?cb=82e8875b286e8790311bb2352f539b0b) * Set connection settings: * **Name:**your choice * **Host Address:** `sra.lightsource.ca` * Port Number: `4000` * Protocol: `NX` * Accept the host verification key * Un-check UDP. * If prompted about proxy settings, choose **Don't use a proxy** (unless you are on a proxied network), Continue * Click 'Add'. ![image-20260624-164134.png](https://bioxas-imaging.lightsource.ca/__attachments/a_23952f426a3a3d6c3ac98c75190b8dfa1f4535a50198bbc5f33f6657118bb2ec/image-20260624-164134.png?cb=c66e800a0afe8f4ef913f0d2e36383a0) ![image-20260624-164241.png](https://bioxas-imaging.lightsource.ca/__attachments/a_96a9697ead9c75b0705191aec09725d1cf057da461c5734f7517e705d614fea3/image-20260624-164241.png?cb=6955399bcd81a01b747b526c14accf71) ### Log Into the Beamline Computer * Double-click the new connection to launch it. * Enter **Username and Password\*\*** * Enter the `nm-` username and password provided by your beamline staff. * Accept the presented certificate fingerprint. * Double-Click the new connection to launch it. * Username/Password: The `nm-` user and password. * Continue through the remaining prompts by selecting **OK** and **Do Not Show Again** where applicable. Leave all default settings unchanged. ![image-20260621-220956.png](https://bioxas-imaging.lightsource.ca/__attachments/a_9de2bb7d590e84e85df401acf05808d4bd82fa3016323e10b2c86257c5e4ed2d/image-20260621-220956.png?cb=53c013744ca26d621708259439a55110) Follow the steps below to adjust the display scale to fit your computer screen: ![image-20260621-221134.png](https://bioxas-imaging.lightsource.ca/__attachments/a_253a9b516123dcc33bcc6ae04778f0ef32eaaf12cfa3b86190cc18d85b5416f2/image-20260621-221134.png?cb=8cd369149774a0b9070e08a0b98d6935) ![image-20260621-221153.png](https://bioxas-imaging.lightsource.ca/__attachments/a_0338f0172c24448b276495caaaaeb367d18c6f3114c4f558335ed66302dac1b8/image-20260621-221153.png?cb=8cc8f1af887670b4ddeeedb165f4134f) ![image-20260621-221223.png](https://bioxas-imaging.lightsource.ca/__attachments/a_db18c1306c524382eca2c44d7d66f7942d424422fa022fd2057f33a8cda40507/image-20260621-221223.png?cb=9c6fa402de179cb0d8c225ba2b648e01) Alternatively, use the shortcut **Ctrl + Alt + F** to go full screen. Or use a shortcut specific to your browser to activate full screen mode. For Microsoft edge, the full screen mode shortcut is the press of the single button F11. * If the computer has multiple displays connected, follow the steps below to switch between the displays (or use the shortcut **Ctrl + Alt + 2** to go to the second display).: ![image-20260621-221243.png](https://bioxas-imaging.lightsource.ca/__attachments/a_ce344158bb6cafa7a48f10d7a6cf81b683ec90e480e747d8052d76fb6a2024d2/image-20260621-221243.png?cb=17514ed2140ee891854766c65c6cb920) ![image-20260621-221302.png](https://bioxas-imaging.lightsource.ca/__attachments/a_0685b2a229bc849ed92ef78b46b82136c71ca1dbb27c59a53bc51b18d63b3d8a/image-20260621-221302.png?cb=02c40f6d67d2f887fabc6844d72e1147) **Precaution**: Please avoid having multiple people remotely connected to the same computer at the same time. When two or more users attempt to control the mouse simultaneously, it can result in unintended clicks and selections. To prevent these issues, ensure that only one person has control of the computer at a time unless coordination between users is required and clearly established. --- language: "en" --- # Sample The BioXAS Imaging beamline capable to analyze a wide range of sample materials, for example: biological, material science, geological, environmental, cultural heritage etc. ## Sample frames dimensions ## Macro-mode * Can fit an array of samples of different size * Mounting a single large sample as large as 25 cm x 25 cm is also feasible. ![image-20250711-225743.png](https://bioxas-imaging.lightsource.ca/__attachments/a_e01304d69e008454bff4e1298319a54f406b718bfd0d9459740ff0c3e886a509/image-20250711-225743.png?cb=675b15dc4aba60b250696e34c34ebf48) ## Micro-mode * Sample holder frame sizes are 1 cm (H) x 2.5 cm (V) and 3 cm (H) x 2c cm (V) | ![image-20250711-225902.png](https://bioxas-imaging.lightsource.ca/__attachments/a_26ed2301a4dd983c0a33c3651a81222373a50b303a07794d97270e8ea7ba1296/image-20250711-225902.png?cb=bb0f6fb1e0d8062d84c62a147c969a77) | |-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| --- language: "en" --- # User Guide ## Where to start? If you are new to synchrotron-based techniques it can be challenging to figure out whether a beamline is suitable for your research. A general approach would be to align the scientific objectives with the main characteristics of a beamline: the absorption energy range of the element(s) of interest, available techniques, and resolution scales. ![image-20250711-224628.png](https://bioxas-imaging.lightsource.ca/__attachments/a_75078095d9eddfb85dc695dbdccb8264977dbd9ead6f256eef8c52f98d2104d2/image-20250711-224628.png?cb=1c4de4a3b77def4f0edda6acce7c6e11) Understanding the principle of XRI is an important step to decide whether this imaging technique would answer your scientific question. Furthermore, examples of data sets collected at our beamline presented under the Publication/Research Highlights section can be also useful to understand the capabilities of the beamline. In addition, under [Readings](https://bioxas-imaging.lightsource.ca/bioxas-imaging/faqs-and-data-transfer), there are links to relevant review papers focusing on the principle and application of synchrotron-based X-ray fluorescence imaging in various fields. **In case you are still unsure and you need clarification, please reach out to the** [**beamline staff.**](https://bioxas-imaging.lightsource.ca/bioxas-imaging/our-team) *** ** * ** *** ## Principle of XRF Imaging In very simple terms, the beamline components will select, deliver and focus the monochromatic (single wavelength) X-ray light onto the sample mounted in the experimental hutch. The sample is moved either by point-by-point or in continuous fly-scanning mode relative to the incident X-ray light. In the former acquisition mode the sample is moved to a position, stops, then resumes moving; however, in the continuous fly scanning mode data are collected as the sample is moving in both directions. The dwell time for the fly scanning mode can also be set shorter (ms), therefore a collection of data with this mode can be a lot shorter in comparison to the point-by-point scan. The dwell time is how much time the X-ray light is allowed on the specific area or pixel. The size of a pixel is usually consistent with the beam size. When the incident X-ray photon hits the sample, the inner shell electrons of atoms in the sample become excited, creating photon electrons and a core hole. The vacant inner shell of an atom is rapidly filled with an outer electron, subsequently releasing X-ray fluorescence photon. This emitted X-ray fluorescence photon's energy is unique for each atom, serving as a fingerprint to identify and study the distribution of elements in various types of samples. The images of elements' distribution in a scanned sample are built by a computer from a single-pixel X-ray fluorescence spectra collected by the X-ray detector. The peaks visible on the computer screen (see image below) would represent the energy of each photon specific to each element detected, the height of the peak indicates number of photons at different energies. ![image-20260618-225119.png](https://bioxas-imaging.lightsource.ca/__attachments/a_ffb5b4eee3e47913f62f8b18a179adff9d390626cfcabd0bbb508dc2da63fd03/image-20260618-225119.png?cb=40489a43c18a08cb0e2838a88c0b2526) ## Techniques ### X-ray fluorescence imaging The BioXAS-Imaging beamline operates between 5 and 21 keV energy range. X-ray fluorescence imaging is one of the main techniques with the capability to provide the distribution of elements at a high spatial resolution and at a relatively short acquisition time. The fast bi-directional fly scanning up to 20 ms dwell time, enables scanning large areas and an adequate number of replicates. ### In situ micro-XAS This technique is an excellent complement to the imaging technique as it allows determining speciation at the micro-scale. Once elemental maps are obtained by the XRI technique, selected spots on the map can be targeted with the energy specific to the element of interest. A scan in energy below and above the absorption edge provides information about the oxidation state of the absorbing element. Coupling imaging with micro-XAS is a powerful method to investigate the composition and speciation of various complex matrixes with minimal or no sample preparation requirement. ### XAS-imaging The BioXAS-Imaging beamline has the capability to scan the same map at energy steps of a XANES spectrum. ![Periodic_table_large.png](https://bioxas-imaging.lightsource.ca/__attachments/a_a9e3c0a466b8a936221f43e4797c3f86c98942185d6f2b1bad153c2363a035fb/Periodic_table_large.png?cb=62b3f4cd7bbf4eb94f3b5b5dd914a535) *** ** * ** *** ## Available resolution-modes There are two resolution modes available, the [macro-mode](https://bioxas-imaging.lightsource.ca/bioxas-imaging/macro-mode) with beam size ranging between 20 to 150 um and [micro-mode](https://bioxas-imaging.lightsource.ca/bioxas-imaging/micro-mode) with focused beam size as small as 5 x 5 um. Based on the desired resolution the user can select between the resolution modes. Furthermore, utilization of both resolution modes during a single beamtime is also possible, but this information needs to be stated in the beamline proposal and communicated with the beamline staff.