{"id":82869,"date":"2026-07-30T12:49:38","date_gmt":"2026-07-30T12:49:38","guid":{"rendered":"https:\/\/www.embl.org\/about\/info\/imaging-centre\/?post_type=vf_event&#038;p=82869"},"modified":"2026-07-30T12:49:39","modified_gmt":"2026-07-30T12:49:39","slug":"autumn-school-on-single-particle-cryo-em-from-sample-to-3d-reconstruction","status":"publish","type":"vf_event","link":"https:\/\/www.embl.org\/about\/info\/imaging-centre\/events\/autumn-school-on-single-particle-cryo-em-from-sample-to-3d-reconstruction\/","title":{"rendered":"Autumn school on single particle cryo-EM: from sample to 3D reconstruction\u00a0"},"content":{"rendered":"\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-fe8c28c6-9f08-437d-83db-93ef79683bbc\" data-vf-js-location-nearest-activation-target=\"\">General Info <\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-96103976-e8dc-496b-a309-87a5e2b4a89c\" data-vf-js-location-nearest-activation-target=\"\">External Speakers<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-737e08e8-ecbe-45d6-bf8a-c0c782d2d4cc\" data-vf-js-location-nearest-activation-target=\"\">Lecture\/Practical Content<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-a9ff2994-ab22-4dfe-b038-2dd56f67a93c\" data-vf-js-location-nearest-activation-target=\"\">Programme<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-73019c48-c318-4ea5-8f19-463968de2b68\" data-vf-js-location-nearest-activation-target=\"\">Practical Information<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-7914244b-6879-4d50-8ca2-7dd132e85081\" data-vf-js-location-nearest-activation-target=\"\">Selection Info<\/a><\/li><\/ul><div class=\"vf-tabs-content\" data-vf-js-tabs-content=\"true\">\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-fe8c28c6-9f08-437d-83db-93ef79683bbc\"><h2>General Info <\/h2>\n<p class=\"wp-block-paragraph\">The EMBL Imaging Centre in collaboration with the Heidelberg University is offering a 5-day autumn school covering all aspects of the single particle cryo-EM workflow. The autumn school will focus on basics of the workflow aimed at PhD students and early career researchers with no or limited experience in single particle cryo-EM.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Content of the course:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Theoretical background and practicals delivered by experts in the field<\/li>\n\n\n\n<li>Sample preparation, grid screening and high-end data collection<\/li>\n\n\n\n<li>Image processing and data analysis<\/li>\n<\/ul>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-96103976-e8dc-496b-a309-87a5e2b4a89c\"><h2>External Speakers<\/h2>\n<div class=\"vf-grid | vf-grid__col-2\"><div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--inline | vf-u-margin__bottom--400\">\n\n    <img decoding=\"async\" width=\"140\" height=\"180\" src=\"https:\/\/www.embl.org\/about\/info\/imaging-centre\/wp-content\/uploads\/2026\/07\/original.jpg\" class=\"vf-profile__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" \/>\n    <h3 class=\"vf-profile__title\" >\n                    <a href=\"https:\/\/www.biochem.mpg.de\/cryoem\" target=\"_self\" class=\"vf-profile__link\">Daniel Bollschweiler <\/a>\n            <\/h3>\n    \n                <p class=\"vf-profile__text\" >\n                Max Planck Institute of Biochemistry, Munich-Martinsried            <\/p>\n    \n    \n      \n\n    \n<\/article>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--inline | vf-u-margin__bottom--400\">\n\n    <img decoding=\"async\" width=\"140\" height=\"180\" src=\"https:\/\/www.embl.org\/about\/info\/imaging-centre\/wp-content\/uploads\/2026\/07\/original-2.jpg\" class=\"vf-profile__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" \/>\n    <h3 class=\"vf-profile__title\" >\n                    <a href=\"https:\/\/www.biochem.mpg.de\/cryoem\" target=\"_self\" class=\"vf-profile__link\">Tillman Sch\u00e4fer <\/a>\n            <\/h3>\n    \n                <p class=\"vf-profile__text\" >\n                Max Planck Institute of Biochemistry, Munich-Martinsried            <\/p>\n    \n    \n      \n\n    \n<\/article>\n\n<\/div>\n<\/div>\n<\/div>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-737e08e8-ecbe-45d6-bf8a-c0c782d2d4cc\"><h2>Lecture\/Practical Content<\/h2>\n<p class=\"wp-block-paragraph\"><strong>Lectures:<\/strong><\/p>\n\n\n\n<ol class=\"wp-block-list\">\n<li>Dirk Flemming (Heidelberg University):&nbsp;<em>Sample and grid preparation for single particle cryo-EM.<\/em>&nbsp;This lecture will discuss general considerations about suitable samples for single particle cryo-EM as well as grid preparation.<\/li>\n\n\n\n<li>Cristina Paulino (Heidelberg University):&nbsp;<em>The transmission electron microscope.<\/em>&nbsp;This lecture will cover basics about the instrument itself with a focus on relevant aspects for its use in single particle cryo-EM data acquisition.<\/li>\n\n\n\n<li>Sebastian Unger (EMBL):&nbsp;<em>Single particle data acquisition.<\/em>&nbsp;General workflow of single particle data acquisition with a focus on practical considerations for microscope operations.<\/li>\n\n\n\n<li>Simon Fromm (EMBL):&nbsp;<em>Single particle data analysis.<\/em>&nbsp;General workflow and concepts of single particle data processing and introduction to the processing software used in the practical.<\/li>\n\n\n\n<li>Daniel Bollschweiler\/Tillman Sch\u00e4fer (external speakers, MPI of Biochemistry, Munich-Martinsried):&nbsp;<em>Title to be determined.<\/em>&nbsp;The lecture will present real-world examples overcoming challenges along the SPA workflow.<\/li>\n<\/ol>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Practicals:<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Trainers: Joe Bartho (EMBL), Rafal Zdanowicz (EMBL), Sebastian Unger (EMBL), Simon Fromm (EMBL), Jan Rheinberger (Heidelberg University)<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Practical 1: Sample preparation (Plunge freezing)<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">To collect single particle cryo-EM data on a cryo-TEM, the biochemically pure sample needs to be embedded into a thin layer of vitrified buffer solution. This is achieved by rapidly plunge freezing the sample after it has been applied onto a support called EM grid.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">For this process, different instruments, instrument settings and sample supports (EM grids) can be used to optimize the result. In the practical, different test samples will be vitrified demonstrating the effect of varying those parameters.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">The participants will have the opportunity to use:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Vitrobot Mark 4 (Thermo Fischer Scientific), plunge freezer generating a gradient of ice thickness<\/li>\n\n\n\n<li>EM GP2 (Leica Microsystems), plunge freezer for single-side blotting<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">Practical 2: Sample loading and screening with a 200 kV cryo-TEM<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">After sample vitrification the EM grid is introduced into the cryo-TEM to evaluate the grid preparation. As it is impossible to predict ideal grid preparation settings, it is important to screen differently prepared grids. Modern cryo-TEMs with a so-called autoloader can take up to 12 grids which can then be screened consecutively without need to manually change the sample. For this, grids prepared in the first practical have to be made ready for loading into the autoloader, a process called clipping.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">The participants will have the opportunity to use:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Clipping of EM grids into cartridges<\/li>\n\n\n\n<li>Loading the clipped grids into 200 kV cryo-TEMs equipped with an autoloader (ThermoScientific Glacios and Talos Arctica microscopes)&nbsp;<\/li>\n\n\n\n<li>Operation of microscopes to collect screening images using SerialEM software<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">Practical 3: High-end single particle data collection on a 300 kV cryo-TEM<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Once a grid suitable for high-end data collection is identified (practical 2), it is transferred into a different cryo-TEM for high-end data collection. The participants will setup automated data collection to collect a data set suitable for image analysis.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">The participants will have the opportunity to use:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>ThermoScientific Titan Krios (300 kV cryo-TEM)<\/li>\n\n\n\n<li>Monitor on-the fly image processing, which serves to asses data quality and eventually optimize data collection<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">Practical 4: Single particle data analysis<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">In this concluding practical, participants will analyze the single particle cryo-EM data collected in practical 3 to reconstruct a 3D volume of the molecule of interest, which was used in practical 1 for EM grid preparation.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">The participants will have the opportunity to use:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>cryoSPARC software installed on a high-performance computing environment<\/li>\n<\/ul>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-a9ff2994-ab22-4dfe-b038-2dd56f67a93c\"><h2>Programme<\/h2>\n<details  class=\"vf-details\" id=\"\"  >\n<summary class=\"vf-details--summary\">\nDay 1 &#8211; Monday 19th October 2026<\/summary>\n<div class=\"acf-innerblocks-container\">\n\n<figure class=\"wp-block-table\"><table class=\"has-fixed-layout\"><thead><tr><th>Time (Europe\/Berlin)<\/th><th>Speaker<\/th><th>Location<\/th><\/tr><\/thead><tbody><tr><td>9:00-9:15<\/td><td><strong>Welcome and Introduction<\/strong><br>Simon Fromm \u2013 EMBL<\/td><td>tbd<\/td><\/tr><tr><td>9:15-09:45<\/td><td><strong>Round table introductions<\/strong><br>All course participants<\/td><td>tbd<\/td><\/tr><tr><td>09:45-11:45<\/td><td><strong>Sample and grid preparation for single particle cryo-EM<\/strong><br>Dirk Flemming \u2013 Heidelberg University<\/td><td>tbd<\/td><\/tr><tr><td>11:45-12:30<\/td><td><strong>Practical on sample preparation by plunge freezing<\/strong><\/td><td>EMBL IC Labs<\/td><\/tr><tr><td>12:30-13:15<\/td><td>Lunch Break<\/td><td>EMBL Canteen<\/td><\/tr><tr><td>13:15-18:15<\/td><td><strong>Practical on sample preparation by plunge freezing<\/strong><\/td><td>EMBL IC Labs<\/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\">\nDay 2 \u2013 Tuesday 20th October 2026<\/summary>\n<div class=\"acf-innerblocks-container\">\n\n<figure class=\"wp-block-table\"><table class=\"has-fixed-layout\"><thead><tr><th>Time (Europe\/Berlin)<\/th><th>Speaker<\/th><th>Location<\/th><\/tr><\/thead><tbody><tr><td>9:00-9:15<\/td><td>Feedback discussion and exchanges on practicals<\/td><td>tbd<\/td><\/tr><tr><td>9:15-11:15<\/td><td><strong>The transmission electron microscope<\/strong><br>Cristina Paulino \u2013 Heidelberg University<\/td><td>tbd<\/td><\/tr><tr><td>11:15-12:30<\/td><td><strong>Practical on sample loading on a TEM with an autoloader module<\/strong><\/td><td>EMBL IC Labs<\/td><\/tr><tr><td>12:30-13:15<\/td><td>Lunch Break<\/td><td>EMBL Canteen<\/td><\/tr><tr><td>13:15-18:15<\/td><td><strong>Practical on grid screening on a 200 kV TEM<\/strong><\/td><td>EMBL IC Labs <\/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\">\nDay 3 \u2013 Wednesday 21st October 2026<\/summary>\n<div class=\"acf-innerblocks-container\">\n\n<figure class=\"wp-block-table\"><table class=\"has-fixed-layout\"><thead><tr><th>Time (Europe\/Berlin)<\/th><th>Speaker<\/th><th>Location<\/th><\/tr><\/thead><tbody><tr><td>9:00-9:15<\/td><td>Feedback discussion and exchanges on practicals<\/td><td>tbc<\/td><\/tr><tr><td>9:15-11:15<\/td><td><strong>Single particle data acquisition<\/strong><br>Sebastian Unger \u2013 Heidelberg University<\/td><td>tbc<\/td><\/tr><tr><td>11:15-12:30<\/td><td><strong>Practical on single particle data collection<\/strong><\/td><td>EMBL IC Labs <\/td><\/tr><tr><td>12:30-13:15<\/td><td>Lunch Break<\/td><td>EMBL Canteen<\/td><\/tr><tr><td>13:15-18:15<\/td><td><strong>Practical on single particle data collection and live pre-processing<\/strong><\/td><td>EMBL IC Labs <\/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\">\nDay 4 \u2013 Thursday 22nd October 2026<\/summary>\n<div class=\"acf-innerblocks-container\">\n\n<figure class=\"wp-block-table\"><table class=\"has-fixed-layout\"><thead><tr><th>Time (Europe\/Berlin)<\/th><th>Speaker<\/th><th>Location<\/th><\/tr><\/thead><tbody><tr><td>9:00-9:15<\/td><td>Feedback discussion and exchanges on practicals<\/td><td>tbd<\/td><\/tr><tr><td>9:15-10:30<\/td><td><strong>Invited Talk<\/strong><br>Daniel Bollschweiler\/Tillman Sch\u00e4fer \u2013 Max Planck Institute of Biochemistry, Munich-Martinsried<\/td><td>tbd<\/td><\/tr><tr><td>10:30-12:30<\/td><td><strong>Image processing &amp; Single particle data analysis<\/strong><br>Simon Fromm \u2013 EMBL<\/td><td>tbd<\/td><\/tr><tr><td>12:30-13:15<\/td><td>Lunch Break<\/td><td>EMBL Canteen<\/td><\/tr><tr><td>13:15-18:15<\/td><td><strong>Practical on single particle data analysis<\/strong><\/td><td>EMBL IC Labs<\/td><\/tr><tr><td>19:00<\/td><td><strong>Course dinner<\/strong><\/td><td>Downtown<\/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\">\nDay 5 \u2013 Friday 23rd October 2026<\/summary>\n<div class=\"acf-innerblocks-container\">\n\n<figure class=\"wp-block-table\"><table class=\"has-fixed-layout\"><thead><tr><th>Time (Europe\/Berlin)<\/th><th>Speaker<\/th><th>Location<\/th><\/tr><\/thead><tbody><tr><td>9:00-12:30<\/td><td><strong>Practical on single particle data analysis<\/strong><\/td><td>tbd<\/td><\/tr><tr><td>12:30-13:15<\/td><td>Lunch Break<\/td><td>EMBL Canteen<\/td><\/tr><tr><td>13:15-13:45<\/td><td><strong>Feedback and closing remarks<\/strong><\/td><td>tbd<\/td><\/tr><\/tbody><\/table><\/figure>\n\n<\/div>\n<\/details>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-73019c48-c318-4ea5-8f19-463968de2b68\"><h2>Practical Information<\/h2>\n<p class=\"wp-block-paragraph\">The course is&nbsp;<strong>limited to 8 participants<\/strong>. For selection purposes, please note that your application will not be considered without CV and a letter of motivation, stating your background and how this course would be beneficial for your future work.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Deadline for registration is September 13th 2026.<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">There is&nbsp;<strong>no registration fee<\/strong>. Travel and accommodation need to be organized and covered by the participants.<\/p>\n\n\n\n<details  class=\"vf-details\" id=\"\"  >\n<summary class=\"vf-details--summary\">\nAccommodation<\/summary>\n<div class=\"acf-innerblocks-container\">\n\n<p class=\"wp-block-paragraph\">Accommodation is&nbsp;<strong>not included<\/strong>. <\/p>\n\n\n\n<p class=\"wp-block-paragraph\">As a guide we have included a list of hotels you may want to consider should you require overnight accommodation:<\/p>\n\n\n\n<figure class=\"wp-block-table is-style-regular\"><table class=\"has-fixed-layout\"><tbody><tr><td><a href=\"https:\/\/hotel-anlage.de\/?lang=en\">Hotel Anlage<\/a><\/td><td><a rel=\"noreferrer noopener\" href=\"https:\/\/www.accorhotels.com\/gb\/hotel-1447-ibis-heidelberg-hauptbahnhof\/index.shtml\" target=\"_blank\">Hotel ibis Heidelberg<\/a><\/td><td><a href=\"https:\/\/www.premierinn.com\/gb\/en\/home.html\">Premier Inn Heidelberg City<\/a><\/td><\/tr><tr><td><a rel=\"noreferrer noopener\" href=\"http:\/\/en.bayrischer-hof-heidelberg.com\/\" target=\"_blank\">Hotel Bayrischer Hof<\/a>&nbsp;<\/td><td><a rel=\"noreferrer noopener\" href=\"http:\/\/en.isg-hotel.de\/\" target=\"_blank\">ISG Hotel<\/a>&nbsp; \u2013&nbsp;<em>nearest hotel to the EMBL Campus<\/em><\/td><td><a rel=\"noreferrer noopener\" href=\"https:\/\/www.staycity.com\/heidelberg\/heidelberg\/\" target=\"_blank\">Staycity Aparthotel Heidelberg<\/a><\/td><\/tr><tr><td><a rel=\"noreferrer noopener\" href=\"https:\/\/www.hotelbb.de\/en\/heidelberg\" target=\"_blank\">B&amp;B Hotel<\/a><\/td><td><a rel=\"noreferrer noopener\" href=\"https:\/\/www.leonardo-hotels.com\/leonardo-hotel-heidelberg-city-center\" target=\"_blank\">Leonardo Hotel Heidelberg City Centre<\/a><\/td><td><a rel=\"noreferrer noopener\" href=\"http:\/\/www.hostelheidelberg.de\/en\/\" target=\"_blank\">Steffi\u2019s Hostel Heidelberg<\/a><\/td><\/tr><tr><td><a rel=\"noreferrer noopener\" href=\"http:\/\/www.the-heidelberg.de\/en\/\" target=\"_blank\">Exzellenz Hotel<\/a>&nbsp;&amp;&nbsp;<a rel=\"noreferrer noopener\" href=\"http:\/\/www.boardinghouse-hd.de\/en\/\" target=\"_blank\">Boarding House<\/a><\/td><td><a rel=\"noreferrer noopener\" href=\"https:\/\/www.meininger-hotels.com\/en\/hotels\/heidelberg\/hotel-heidelberg-central-station\/\" target=\"_blank\">Meininger Heidelberg<\/a><\/td><td><a rel=\"noreferrer noopener\" href=\"https:\/\/4-jahreszeiten.de\/\" target=\"_blank\">Hotel Vier Jahreszeiten Heidelberg<\/a><\/td><\/tr><tr><td><a rel=\"noreferrer noopener\" href=\"http:\/\/www.hollaender-hof.de\/index.php\/en\/\" target=\"_blank\">Hotel Holl\u00e4nder Hof<\/a>&nbsp;<\/td><td><a rel=\"noreferrer noopener\" href=\"http:\/\/www.hotel-monpti.de\/en\/\" target=\"_blank\">Hotel Monpti<\/a><\/td><td><\/td><\/tr><\/tbody><\/table><\/figure>\n\n<\/div>\n<\/details>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-7914244b-6879-4d50-8ca2-7dd132e85081\"><h2>Selection Info<\/h2>\n<p class=\"wp-block-paragraph\">Selected participants will be announced on September 21st\u00a02026. For selection purposes, please note that your application will not be considered without CV and a letter of motivation, stating your scientific background, how this course would be beneficial for your future work.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">The participants are selected based on EMBL\u2019s course and conferences inclusive criteria (which can be found on the course and conference homepage) and are summarized below:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Selection of candidates is based on there being a good match between the learning objectives of the course and the stated needs of the candidate, as well as accessibility to the instruments\/workflows to the candidate after the course.<\/li>\n\n\n\n<li>Depending on the applicants, the course will not welcome more than 25% of participants from the same institution\u2019s host country. Same institutions have to be avoided in order to ensure a broader geographical distribution of the knowledge learned during the course.<\/li>\n\n\n\n<li>Aim for gender balance when selecting the final participants (at least 30% of the minority gender).&nbsp;<\/li>\n\n\n\n<li>Applications from organisers, speakers, or trainer laboratories are not prioritised. <\/li>\n<\/ul>\n<\/section>\n<\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"parent":0,"menu_order":0,"template":"","embl_taxonomy":[],"class_list":["post-82869","vf_event","type-vf_event","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"vf_event_start_date":{"value":"20261019","formatted":"19 October 2026"},"vf_event_end_date":{"value":"20261023","formatted":"23 October 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