{"id":57,"date":"2025-06-10T23:01:48","date_gmt":"2025-06-10T23:01:48","guid":{"rendered":"https:\/\/www.embl.org\/groups\/x-ray-imaging\/?page_id=57"},"modified":"2025-07-30T07:03:17","modified_gmt":"2025-07-30T07:03:17","slug":"beamline-p14","status":"publish","type":"page","link":"https:\/\/www.embl.org\/groups\/x-ray-imaging\/beamline-p14\/","title":{"rendered":"Imaging at P14"},"content":{"rendered":"\n<div class=\"vf-grid | vf-grid__col-3\"><div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<p>We have developed a high-throughput workflow for imaging of biological tissue. As a result, there are defined ways of preparing your samples.&nbsp;The following section provides comprehensive details regarding the imaging parameters and on-site image acquisition protocols.<\/p>\n\n\n\n<div style=\"height:35px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<div class=\"vf-tabs\"><ul class=\"vf-tabs__list\" data-vf-js-tabs=\"true\"><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-sample-sizes-and-acquisition-times\" data-vf-js-location-nearest-activation-target=\"\">Sample sizes and acquisition times<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-beamline-parameters\" data-vf-js-location-nearest-activation-target=\"\">Beamline parameters<\/a><\/li><\/ul><div class=\"vf-tabs-content\" data-vf-js-tabs-content=\"true\">\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-sample-sizes-and-acquisition-times\"><h2 class=\"vf-u-sr-only\">Sample sizes and acquisition times<\/h2>\n<div class=\"vf-grid | vf-grid__col-2\"><div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<p>The acquisition protocol consists of acquiring a tomographic dataset of the sample at each of four different sample-camera distances. Phase retrieval from this data is performed using the \u201cholotomography\u201d approach, after which tomographic reconstruction is performed.<\/p>\n\n\n\n<p>For suitably small samples (at most 1.3 mm diameter and 1.0 mm height), a single 180-degree tomographic scan is performed at each distance.<\/p>\n\n\n\n<p>For somewhat larger samples (up to 2.1 mm diameter, 1.0 mm height), the system can be set up to perform 360-degree, off-centre tomography. Samples with a greater height or diameter can also be scanned by repeatedly performing region-of-interest tomography (\u201ctiling\u201d acquisition) and stitching the resulting 3D data.<\/p>\n\n\n\n<p>This is easy to do if tiling is only required for the vertical direction, but tiling in multiple dimensions is more complex and also results in the generation of a large amount of data. Furthermore, samples in aqueous solution tend to generate gas bubbles in the synchrotron beam, which often affects image quality. The probability of bubbles appearing increases with the length of the scan, and thus the number of tiling steps.<\/p>\n\n\n\n<p>The figure below gives a qualitative comparison of the available acquisition techniques.<\/p>\n\n\n\n<figure class=\"vf-figure wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"572\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/sample_sizes2-1024x572.png\" alt=\"Infographic detailing achievable sample volume, sample throughput per hour, dataset size, difficulty, and compatibility with aqueous sample for different acquisition techniques.\" class=\"wp-image-417\" srcset=\"https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/sample_sizes2-1024x572.png 1024w, https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/sample_sizes2-300x167.png 300w, https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/sample_sizes2-768x429.png 768w, https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/sample_sizes2.png 1449w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><figcaption class=\"vf-figure__caption\">Comparison of different acquisition techniques<\/figcaption><\/figure>\n\n<\/div>\n<\/div>\n<\/div>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-beamline-parameters\"><h2>Beamline parameters<\/h2>\n<div class=\"vf-grid | vf-grid__col-2\"><div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<details  class=\"vf-details\" id=\"\"  >\n<summary class=\"vf-details--summary\">\nThe X-ray beam<\/summary>\n<div class=\"acf-innerblocks-container\">\n\n<p>P14 is an undulator beamline, which uses a double-crystal monochromator to generate monochromatic radiation of photon energies between 8 and 32 keV. Energies typically used for imaging are 18 and 23.5 keV, selected depending on the dimensions and composition of the sample. Energies between 26.5 and 32 keV are available on special request.<\/p>\n\n\n\n<p>The size of the beam at the position of the sample is about 1.3 mm x 1.0 mm (width x height), which is the primary limitation for the size of imaged samples (see also the section \u201cDetection system\u201d below).<\/p>\n\n<\/div>\n<\/details>\n\n\n\n<details  class=\"vf-details\" id=\"\"  >\n<summary class=\"vf-details--summary\">\nSample stage<\/summary>\n<div class=\"acf-innerblocks-container\">\n\n<p>The MD3 diffractometer is used as a rotation stage for tomographic imaging. The rotation axis is oriented vertically, and the samples are mounted downward, i.e. \u201changing\u201d from the attachment point. The sample mount is based on the SPINE magnetic sample holder developed for macromolecular crystallography (MX). The diffractometer features a visible-light microscope which is aligned with the X-ray beam that enables, in combination with a graphical user interface, convenient alignment of samples with the beam before enabling X-rays.&nbsp; Samples can be mounted manually or using the sample changer described below.<\/p>\n\n<\/div>\n<\/details>\n\n\n\n<details  class=\"vf-details\" id=\"\"  >\n<summary class=\"vf-details--summary\">\nDetection system<\/summary>\n<div class=\"acf-innerblocks-container\">\n\n<p>We use an Optique Peter X-ray microscope in combination with a PCOedge 4.2 sCMOS camera (2048 \u00d7 2048 pixels, 6.5 \u03bcm pixel size, max. 100 Hz frame rate) and an LSO:Tb on YbSO scintillator (thickness 8-10 \u03bcm). The microscope features three objectives, providing 4x, 10\u00d7 or 20\u00d7 magnification. For 4\u00d7 and 10\u00d7, the effectively usable field of view is however limited by the extent of the beam (about 1.3 mm horizontal \u00d7 1.0 mm vertical).<\/p>\n\n\n\n<p>For the majority of experiments, we recommend the use of the 10\u00d7 objective, but this can be discussed at the time of proposal submission and\/or in the run up to your beamtime.<\/p>\n\n\n\n<figure class=\"wp-block-table\"><table class=\"has-fixed-layout\"><tbody><tr><td><strong>Objective<\/strong><\/td><td><strong>Usable field of view (H x V)<\/strong><\/td><td><strong>Pixel size<\/strong><\/td><\/tr><tr><td>10\u00d7<\/td><td>1.3 mm \u00d7 1.0 mm<\/td><td>0.65 \u03bcm<\/td><\/tr><tr><td>20\u00d7<\/td><td>0.67 mm \u00d7 0.67 mm<\/td><td>0.325 \u03bcm<\/td><\/tr><tr><td>4\u00d7<\/td><td>1.3 mm \u00d7 1.0 mm<\/td><td>1.625 \u03bcm<\/td><\/tr><\/tbody><\/table><\/figure>\n\n<\/div>\n<\/details>\n\n\n\n<details  class=\"vf-details\" id=\"\"  >\n<summary class=\"vf-details--summary\">\nUser interface<\/summary>\n<div class=\"acf-innerblocks-container\">\n\n<p>The user primarily interacts with the beamline via the MXCuBE graphical interface in \u201cimaging\u201d mode. This software allows sample centring, adjustment of a wide range of setup and acquisition parameters, and starting image acquisition. Manipulation of various motorised stages required for aligning the setup and other tasks can be performed via a second graphical interface, or alternatively, directly interacting with the TINE beamline control system through a command line interface. Additional tools exist for use by beamline staff for diagnostics and specialised tasks.<\/p>\n\n<\/div>\n<\/details>\n\n\n\n<details  class=\"vf-details\" id=\"\"  >\n<summary class=\"vf-details--summary\">\nSPINE sample mounting system<\/summary>\n<div class=\"acf-innerblocks-container\">\n\n<p>At P14, we use the SPINE system for mounting samples, which is widely used in macromolecular crystallography (MX). This system consists of:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>standardised goniometer bases on which the samples are mounted, and which attach magnetically to the attachment point of the diffractometer,<\/li>\n\n\n\n<li>plastic caps (\u201cCryoVials\u201d), which cover the sample when not in use, and which are also magnetically attached to the base, and<\/li>\n\n\n\n<li>\u201cpucks\u201d, cylindrical containers holding up to ten samples each.<\/li>\n<\/ul>\n\n\n\n<p>We commonly use 3D-printed adapters to attach samples to the SPINE bases. The MARVIN sample changing system (see below) is designed around the SPINE system.<\/p>\n\n\n\n<p>A reasonable number of SPINE bases and caps can be obtained from us upon prior request. For larger experiments with big sample cohorts, SPINE bases and caps can be acquired here:<\/p>\n\n\n\n<a href=\"https:\/\/www.jenabioscience.com\/crystallography\/data-collection\/cryo-and-room-temperature-crystallography\/goniometer-bases\/type-b5\" target=\"_blank\">\n<button class=\"vf-button vf-button--link\">Goniometer Base B5 &#8211; www.jenabioscience.com<\/button>\n<\/a>\n<!--\/vf-button-->\n\n\n\n\n<a href=\"https:\/\/www.jenabioscience.com\/crystallography\/data-collection\/cryo-and-room-temperature-crystallography\/magnetic-cryovials\" target=\"_blank\">\n<button class=\"vf-button vf-button--link\">Gonimeter Cap &#8211; www.jenabioscience.com<\/button>\n<\/a>\n<!--\/vf-button-->\n\n\n\n\n<div class=\"vf-grid | vf-grid__col-2\"><div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<figure class=\"vf-figure wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"768\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/IMG_1139-1024x768.jpeg\" alt=\"\" class=\"wp-image-370\" srcset=\"https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/IMG_1139-1024x768.jpeg 1024w, https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/IMG_1139-300x225.jpeg 300w, https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/IMG_1139-768x576.jpeg 768w, https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/IMG_1139-1536x1152.jpeg 1536w, https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/IMG_1139-2048x1536.jpeg 2048w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><figcaption class=\"vf-figure__caption\"><a href=\"https:\/\/www.mitegen.com\/product\/spine-pucks-sc3-baskets\/\" data-type=\"link\" data-id=\"https:\/\/www.mitegen.com\/product\/spine-pucks-sc3-baskets\/\">MiTeGen SPINE puck (SC3 Basket)<\/a><\/figcaption><\/figure>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<figure class=\"vf-figure wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"768\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/IMG_1140-1024x768.jpeg\" alt=\"\" class=\"wp-image-371\" srcset=\"https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/IMG_1140-1024x768.jpeg 1024w, https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/IMG_1140-300x225.jpeg 300w, https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/IMG_1140-768x576.jpeg 768w, https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/IMG_1140-1536x1152.jpeg 1536w, https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/IMG_1140.jpeg 2034w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><figcaption class=\"vf-figure__caption\"><a href=\"https:\/\/www.mitegen.com\/product\/b5-goniometer-bases\/\" data-type=\"link\" data-id=\"https:\/\/www.mitegen.com\/product\/b5-goniometer-bases\/\">MiTeGen SPINE Goniometer base (B5)<\/a><\/figcaption><\/figure>\n\n<\/div>\n<\/div>\n<\/div>\n\n<\/div>\n<\/details>\n\n\n\n<details  class=\"vf-details\" id=\"\"  >\n<summary class=\"vf-details--summary\">\nAutomatic sample mounting<\/summary>\n<div class=\"acf-innerblocks-container\">\n\n<p>The \u201cMARVIN\u201d sample changing system is available for the transfer of samples from storage to the diffractometer for imaging, and is controlled via the MXCuBE interface. The storage has a capacity of 17 pucks, i.e., up to 170 samples.<\/p>\n\n\n\n<figure class=\"vf-figure wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"699\" height=\"705\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/Marvin.png\" alt=\"\" class=\"wp-image-374\" srcset=\"https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/Marvin.png 699w, https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/Marvin-297x300.png 297w, https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/Marvin-150x150.png 150w\" sizes=\"auto, (max-width: 699px) 100vw, 699px\" \/><figcaption class=\"vf-figure__caption\">MARVIN mounting a sample on the MD3 Goniometer. And robot gripper, samples Puck storage plate on the right. <br>Taken from <a href=\"https:\/\/accelconf.web.cern.ch\/pcapac2018\/posters\/thp03_poster.pdf\" data-type=\"link\" data-id=\"https:\/\/accelconf.web.cern.ch\/pcapac2018\/posters\/thp03_poster.pdf\">Ristau, U., et al. &#8220;Marvin Update\u2013the EMBL\u2013Hamburg Robotic Sample Changer.&#8221;<\/a><\/figcaption><\/figure>\n\n<\/div>\n<\/details>\n\n\n\n<details  class=\"vf-details\" id=\"\"  >\n<summary class=\"vf-details--summary\">\nData acquisition and processing<\/summary>\n<div class=\"acf-innerblocks-container\">\n\n<p>The acquisition protocol consists of acquiring four tomographic datasets of the sample at four different sample-camera distances (73\u201392 mm).<\/p>\n\n\n\n<p>After collection, the beamline compute cluster automatically performs flat-field correction, \u201cholotomography\u201d phase retrieval, and 3D reconstruction of the data (using the \u201cgridrec\u201d algorithm). The processing time is one minute for a standard scan, and the results can be viewed immediately afterwards. If tiled acquisition is performed, the individual datasets are automatically stitched as soon as reconstruction is complete. This usually also takes only a few minutes.<\/p>\n\n\n\n<figure class=\"vf-figure wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"425\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/data_processing-1024x425.png\" alt=\"\" class=\"wp-image-377\" srcset=\"https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/data_processing-1024x425.png 1024w, https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/data_processing-300x124.png 300w, https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/data_processing-768x319.png 768w, https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/data_processing-1536x637.png 1536w, https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-content\/uploads\/2025\/07\/data_processing.png 2025w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><figcaption class=\"vf-figure__caption\">The HiTT pipeline. For each sample, four different data collections at increasing propagation distances are performed. Subsequently, the data processing is triggered automatically.<\/figcaption><\/figure>\n\n<\/div>\n<\/details>\n\n<\/div>\n<\/div>\n<\/div>\n<\/section>\n<\/div><\/div>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-card vf-card--brand vf-card--bordered vf-u-margin__bottom--800\" default>\n  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n              <a class=\"vf-card__link\" href=\"https:\/\/docs.google.com\/document\/d\/1S1gcAWUgnBjLN3DEGzxoW3rrT6zuAO2GPf5dRzc5_cw\/edit?usp=share_link\">\n      P14 User Manual       <svg aria-hidden=\"true\" class=\"vf-card__heading__icon | vf-icon vf-icon-arrow--inline-end\" width=\"1em\" height=\"1em\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\">\n          <path d=\"M0 12c0 6.627 5.373 12 12 12s12-5.373 12-12S18.627 0 12 0C5.376.008.008 5.376 0 12zm13.707-5.209l4.5 4.5a1 1 0 010 1.414l-4.5 4.5a1 1 0 01-1.414-1.414l2.366-2.367a.25.25 0 00-.177-.424H6a1 1 0 010-2h8.482a.25.25 0 00.177-.427l-2.366-2.368a1 1 0 011.414-1.414z\" fill=\"currentColor\" fill-rule=\"nonzero\"><\/path>\n       <\/svg>\n        <\/a>\n          <\/h3>\n                <p class=\"vf-card__text\">How to collect your imaging data.<\/p>\n      <\/div>\n<\/article>\n\n\n\n\n<p><\/p>\n\n\n\n<div class=\"vf-content--grey-box\">\n\n\n\n<article class=\"vf-summary vf-summary--publication\">\n    <h3 class=\"vf-summary__title\">\n        <a href=\"https:\/\/journals.iucr.org\/s\/issues\/2024\/01\/00\/ay5623\/index.html\" class=\"vf-summary__link\">\n        High Throughput Tomography (HiTT) on EMBL beamline P14 on PETRA III        <\/a>\n    <\/h3>\n    <p class=\"vf-summary__author\">\n      Albers, J., Nikolova, M., Svetlove, A., Darif, N., Lawson, M. J., Schneider, T. R., Schwab, Y., Bourenkov, G., and Duke, E.    <\/p>\n    <p class=\"vf-summary__source\">\n    Synchrotron Radiation, 31(1), 186-194        <span class=\"vf-summary__date\">2024<\/span>\n    <\/p>\n\n    <p class=\"vf-summary__text\">\n    DOI: 10.1107\/S160057752300944X    <\/p>\n<\/article>\n\n\n\n<\/div>\n\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<div class=\"vf-grid | vf-grid__col-1\"><div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<style>\n.vf-content--grey-box {\n  background-color: #fafafa;\n  padding: 1.5rem;\n  border-radius: 6px;\n  margin-top: 1rem;\n  margin-bottom: 2rem;\n}\n<\/style>\n\n\n\n<style>\n.wp-block-table {\n  width: 100%;\n  overflow-x: auto;\n}\n\n.wp-block-table table {\n  width: 100%;\n  table-layout: auto;\n  border-collapse: collapse;\n}\n\n.wp-block-table th,\n.wp-block-table td {\n  word-wrap: break-word;\n  white-space: normal;\n}\n<\/style>\n\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":2,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"template-title-left-aligned.php","meta":{"_acf_changed":false,"footnotes":""},"embl_taxonomy":[],"class_list":["post-57","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-json\/wp\/v2\/pages\/57","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-json\/wp\/v2\/comments?post=57"}],"version-history":[{"count":104,"href":"https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-json\/wp\/v2\/pages\/57\/revisions"}],"predecessor-version":[{"id":809,"href":"https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-json\/wp\/v2\/pages\/57\/revisions\/809"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-json\/wp\/v2\/media?parent=57"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.embl.org\/groups\/x-ray-imaging\/wp-json\/wp\/v2\/embl_taxonomy?post=57"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}