[3dem] Workshop on the use of Scipion in CryoEM facilities

Wed Sep 17 14:12:26 PDT 2025

Hello,

Will the talks be recorded and accessible later?

Thank you,

William J Nicolas - PhD

From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of 3dem-request at ncmir.ucsd.edu <3dem-request at ncmir.ucsd.edu>
Date: Wednesday, September 17, 2025 at 10:33 AM
To: 3dem at ncmir.ucsd.edu <3dem at ncmir.ucsd.edu>
Subject: 3dem Digest, Vol 217, Issue 16
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Today's Topics:

   1. Workshop on the use of Scipion in CryoEM facilities
      (Carlos Oscar Sorzano)
   2. post-doc positions open in Palm Beach, Florida (Tina Izard)
   3. Cryo-Electron Tomography Virtual Course November 3rd - 6th
      2025 (Oksana Degtjarik)

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Message: 1
Date: Wed, 17 Sep 2025 16:27:54 +0200
From: Carlos Oscar Sorzano <coss at cnb.csic.es>
To: 3demmethods at cnb.csic.es, 3dem <3dem at ncmir.ucsd.edu>,
        CCPEM at JISCMAIL.AC.UK
Subject: [3dem] Workshop on the use of Scipion in CryoEM facilities
Message-ID: <ea2409eb-c212-4822-ba16-5b67752c95e7 at cnb.csic.es>
Content-Type: text/plain; charset=UTF-8; format=flowed

Dear all,

on October 30th and 31st we will hold our annual workshop of Scipion for
facilities. This meeting aims to gather feedback and showcase how
different facilities are using Scipion, demonstrating its capabilities
and benefits for Cryo-EM centers. The event will feature talks and ample
time for discussion, aiming to share experiences with Scipion, discuss
operational methodologies, and highlight new developments that can
enhance our community?s daily workflow.

You will find all the details at https://urldefense.com/v3/__https://i2pc.es/facilities-2025/__;!!Mih3wA!B-2gWUzQOo-SNojXi2np_JbU3cpILB0yA8yCoupHk-NuBUpLAQMwO_kiRogaU-_-SqMpsOt0ffvi1GdoPw$<https://urldefense.com/v3/__https:/i2pc.es/facilities-2025/__;!!Mih3wA!B-2gWUzQOo-SNojXi2np_JbU3cpILB0yA8yCoupHk-NuBUpLAQMwO_kiRogaU-_-SqMpsOt0ffvi1GdoPw$>

Kind regards, Carlos Oscar

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Message: 2
Date: Wed, 17 Sep 2025 15:22:10 +0000
From: Tina Izard <izard at scripps.edu>
To: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
Subject: [3dem] post-doc positions open in Palm Beach, Florida
Message-ID:
        <SA3PR11MB7553FDA72705972DECDFFDDFBC17A at SA3PR11MB7553.namprd11.prod.outlook.com>

Content-Type: text/plain; charset="windows-1252"

Post-doctoral Associate positions are immediately available in Tina Izard?s cell adhesion laboratory

Join a dynamic structural biology group at the UF-Scripps, where we push the boundaries of molecular visualization and membrane biology. Our lab integrates cutting-edge cryoEM, membrane biophysics, and infection/immunity research to redefine how receptors like integrins, GPCRs, and adhesion complexes are regulated. This position offers the opportunity to drive high-impact projects, publish in top journals, and grow your expertise in method development and biological discovery.

About this opportunity

Successful candidates will work in a cutting-edge research environment with new state-of-the-art facilities. The laboratory has outstanding cell biology, molecular biology, protein expression, purification, biochemistry, cryogenic electron microscopy, and protein crystallography facilities. The laboratory has access to many exceptional Cores, facilitating basic research and drug development. The unique infrastructure includes the application of unique chemical, genomic, proteomic, informatics, and high-throughput screening and engineering tools for discovering novel biomolecules.

CryoEM at UF-Scripps

Tina Izard installed the first 300 kV cryo Atomic Resolution Microscope (cryoARM300) in the Americas (https://urldefense.com/v3/__https://www.youtube.com/watch?v=xdVxAN8xy1w&feature=youtu.be__;!!Mih3wA!DDo1nFVbZw6S4jOXirodGuI4tfElR-MrFp5p5d3_XBSii1Ay4QH36lsh5mHbDg6_paW328YN-3_jpFHRuCg$ ) and has plenty of microscope time dedicated to the post-doctoral associates. This state-of-the-art transmission electron microscope is a 300 kV high-resolution microscope capable of carrying out cryogenic electron microscopy studies by providing atomic resolution for structural studies involving single particle analyses. The transmission electron microscope is equipped with a new and improved Gatan K3 direct electron detector camera with better DQE, a larger field of view (24 Megapixels ? 5,760 x 4,092), and faster (3.75 times that of the K2 camera). The direct detection devices are exquisitely sensitive, produce high signal-to-noise images, and are ideal for high-resolution studies.

X-ray crystallography at UF-Scripps

The lab has access to SER-CAT beamlines at Sector 22 of the Advanced Photon Source, including modern insertion device lines (22-ID-D, variable wavelength, and 22-ID-E, fixed wavelength) as well as a bending magnet line (22-BM) for macromolecular crystallography. These facilities are equipped with updated optics and detectors, and fall under current APS upgrades, ensuring high performance for structural biology projects.

The lab has access to a HighFlux X-ray diffraction system, specifically a Rigaku MicroMax-007 HF, a second-generation microfocus rotating anode generator, and a mar345 Image Plate detector. An Osmic VariMax optics system and the Proteros Free Mounting System can be used to control the humidity and optimize diffraction characteristics, including resolution, mosaicity, anisotropy, and reduced X-ray background.

Intellectual environment

UF-Scripps shares its Jupiter campus with the Max Planck Florida Institute for Neuroscience (MPFI), North America's only Max Planck Institute. MPFI is internationally recognized for innovation in imaging and neuroscience, and its presence creates a unique, highly collaborative research environment. Postdocs benefit from joint seminars, shared facilities, interdisciplinary collaborations, and daily interaction with world-class scientists across structural biology, chemical biology, and neuroscience. This close partnership expands opportunities for discovery and professional growth beyond what most academic campuses offer.

Why Jupiter, Florida?

UF-Scripps is located in Jupiter, Florida, a vibrant coastal community in Palm Beach County. Jupiter offers an outstanding quality of life with year-round sunshine, beautiful beaches, outdoor recreation, and a safe, family-friendly atmosphere. The area combines the advantages of a relaxed lifestyle with proximity to Miami and Orlando for cultural and professional opportunities. Florida has no state income tax, making post-doctoral salaries go further, and the cost of living in northern Palm Beach County is favorable compared to many other significant research hubs. The campus itself is part of a growing biotech corridor that includes Max Planck Florida, providing an interdisciplinary, collaborative environment with cutting-edge science in an exceptional location.

--
Dr. T. Izard
Professor
Cell Adhesion Laboratory
Member, Scientific Advisory Group, UF ICBR EM Core
Board Member, SER-CAT, Advanced Photon Source, Argonne National Laboratory

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Message: 3
Date: Wed, 17 Sep 2025 16:05:01 +0000
From: Oksana Degtjarik <O.Degtjarik at leeds.ac.uk>
To: "ccpem at jiscmail.ac.uk" <ccpem at jiscmail.ac.uk>
Subject: [3dem] Cryo-Electron Tomography Virtual Course November 3rd -
        6th     2025
Message-ID:
        <PAXPR03MB7936557A67268C72C74246F4B517A at PAXPR03MB7936.eurprd03.prod.outlook.com>

Content-Type: text/plain; charset="us-ascii"

Dear Community,

We are pleased to announce the beginners Cryo-Electron Tomography virtual course taking place from the 3th - 6th of November 2025 as part of the UK community-led training program in cryo-EM funded by Wellcome and the MRC.

Hosted by the University of Leeds (ABSL), eBIC at Diamond Light Source, the University of Leicester, and Birkbeck, University of London, this four-day course is aimed at early career researchers with little or no prior experience in cryo-electron tomography that plan to incorporate cryo-ET into their research. It will introduce participants to the cryo-ET workflow, covering sample preparation, sample thinning via FIB-SEM, tilt-series acquisition, and image analysis. Participants will receive hands-on training in small groups on a Titan Krios, guided by expert instructors, and will observe live demonstrations of cryo-FIB/SEM techniques for lamella milling and lift-outs, as well as cryo-ET data processing in RELION 5.
Please register your interest using this form<https://urldefense.com/v3/__https://forms.office.com/e/SisJcP3BQC__;!!Mih3wA!GxS02J2lcrxFFs9UqeAIM1mINHEMdaw9RjPytGCJoE9rH-KG98pEg9eA3JEqKf9o6WyX33o_pIZwuYacPOvmWbn6fok$ > by the 8th of October.

We look forward to seeing you soon!

Best wishes,
Oksana Degtjarik (on the behalf of the organisers)

Wellcome Trust and MRC (218785/Z/19/Z) national cryo-EM training grant
https://urldefense.com/v3/__https://astbury.leeds.ac.uk/facilities/wellcome-mrc-training-in-cryoem/__;!!Mih3wA!GxS02J2lcrxFFs9UqeAIM1mINHEMdaw9RjPytGCJoE9rH-KG98pEg9eA3JEqKf9o6WyX33o_pIZwuYacPOvmN3UsjOA$<https://urldefense.com/v3/__https:/astbury.leeds.ac.uk/facilities/wellcome-mrc-training-in-cryoem/__;!!Mih3wA!GxS02J2lcrxFFs9UqeAIM1mINHEMdaw9RjPytGCJoE9rH-KG98pEg9eA3JEqKf9o6WyX33o_pIZwuYacPOvmN3UsjOA$>

  Oksana Degtjarik (she/her)
  Cryo-EM scientist
[A green and purple logo  Description automatically generated]
   Astbury Biostructure Laboratory
   Cryo-EM Facility
   Roger Stevens 6.80
   University of Leeds
   LS2 9JT Leeds

   E: o.degtjarik at leeds.ac.uk<mailto:odegtjarik at leeds.ac.uk>

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