workshop Archives - I2PC - Instruct Image Processing Center

Scipion for facilities Workshop. October 29 – 30, 2026

June, 2026July, 2026 by blanca

Cryo-EM Facilities Meeting 2026

Workshop Information

Meeting Information

Venue	Hybrid
Location	National Center for Biotechnology (CNB), Madrid, Spain
Date	October 29–30, 2026
Contact	I2PC – Instruct Image Processing Center

Aim

This meeting will gather feedback and showcase how different facilities are using Scipion in Cryo-EM centers. The event will include talks and discussion time to share experiences, review operational methodologies, present new developments, and improve the community’s daily workflow.

Conditions

The workshop will take place at the Spanish National Centre for Biotechnology (CNB) in Madrid and can be attended in person or remotely. No programming skills are required. Online sessions will use CSIC Conecta; please check your browser at conecta.csic.es .

Program

The detailed agenda is currently being finalized and will be announced shortly. We start the day at:

Thursday 29 October – Hybrid
10:00 – 10:30	Welcome and assistant’s introduction
10:30 – 11:00	Scipion SPA in a live acquisition with several workflows; an overview – Alberto Garcia [CNB-CSIC-Madrid]
11:00 – 11:30	SBGrid: Research Computing Support for Structural Biology – Using Scipion in SBGrid – Estrella Fernandez [SBGrid Consortium, Boston]
11:30 – 12:00	Coffee break
12:00 – 12:30	Screening feedback with in live processing. Beyond the in live pipeline – Alberto Garcia [CNB-CSIC-Madrid]
12:30 – 13:00	TBA
13:00 – 14:00	Lunch
14:00 – 14:30	TBA
14:30 – 15:00	TBA
15:00 – 15:30	TBA
15:30 – 16:00	TBA
Friday 30 October – Hybrid
10:00 – 10:30	Live image processing with ScipionTomo for facilities – José Luis Vilas and Jorge Jiménez [CNB-CSIC, Madrid]
10:30 – 11:00	Cryo-EM in CNPEM – Rodrigo Villares [CNPEM, Campinas]
11:00 – 11:30	Implementing On-the-Fly Tomography Data Processing with Scipion3 at DCI Lausanne – Emiko Uchikawa [Dubochet Center for Imaging (DCI), Lausanne]
11:30 – 12:00	The CryoEM CNB-CSIC facility setup; EMHub, IRODS, FandanGO
12:00 – 12:30	Coffee break
12:30 – 13:00	Cryo-EM for Translational Biomedicine: Insights from the IBMB-CSIC Platform – Pablo Guerra [Ibmb – Barcelona]
13:00 – 13:30	The Screening Gateway: Building Portugal’s First Talos 12 Cryo-EM Facility – Dmitry Semchonok [ITQB Lisboa]
13:30 – 14:00	Integrating Scipion into the European Synchrotron Infrastructure – Ludovic Broche [ESRF Grenoble]
14:00	Lunch

Registration is free for all attendees.

Further details, such as class locations, meeting links, title updates, and instructions for reaching the centre, will be provided in the weeks leading up to the workshop.

Scipion for facilities Workshop. October 30 – 31, 2025

July, 2025February, 2026 by Oscar Saiz

Dates: October 30-31, 2025

Venue: hybrid

National Center for Biotechnology (CNB), Madrid, Spain.
Madrid, October 30 – 31, 2025

Aim:

The aim of this meeting is 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.

Conditions:

The workshop will be held on October 30 and 31 at the Spanish National Centre for Biotechnology (CNB) in Madrid, Spain. It can be attended either in person or remotely. No programming skills are required. We will use the CSIC Conecta video conferencing system for the online sessions — please verify your browser works at https://conecta.csic.es/.

Program:

We start the day at:

AGENDA

Thursday 30th October – Hybrid
10:00 – 10.30	Welcome and assistant’s introduction
10:30 – 11:00	An Unattended Image Processing Pipeline for On-the-Fly Quality Assessment and 3D Exploration in Cryo-EM – Daniel Marchán (CNB-CSIC, Madrid)
11:00 – 11:30	Deployment of Scipion in clusters (with and without containers) – Lola Sánchez and Mikel Iceta (CNB-CSIC, Madrid)
11:30 – 12:00	Coffee break
12:00 – 12:30	Enhancing screening in acquisition time scipion-em-smartscope – Alberto García (CNB-CSIC, Madrid)
12:30 – 13:00	nextPYP: a web-based platform for monitoring cryo-EM and cryo-ET sessions in real-time – Alberto Bartesaghi (Duke University – Computer Science and Biochemistry)
13:00 – 14:00	Lunch
14:00 – 14:30	FAIR data collection with the Open Science Community for Electron Microscopy (OSC-EM) metadata standard – Spencer Bliven (Paul Scherrer Institute)
14:30 – 15:00	Facilitating cryo-EM single-particle and tomography data analysis with EMhub – José Miguel de la Rosa Trevin (St. Jude Children’s Research Hospital, Memphis)
15:00 – 15:30	The CryoEM CNB-CSIC facility setup: EMhub, iRODS, OSCEM – Lola Sánchez and Irene Sánchez (CNB-CSIC, Madrid)
15:30 – 16:00	Discussion and conclusions
Friday 31st October – Hybrid
10.00 – 10:30	Live image processing with ScipionTomo for facilities – José Luis Vilas and Jorge Jiménez (CNB-CSIC, Madrid)
10:30 – 11:00	Balancing CryoSPA and CryoET: Building Skills and Innovation in a BSL-2 Facility – Carolin Seuring (Cryo-EM Technology Platform at CSSB Hamburg)
11:00 – 11:30	Four years of progress at the cryo-EM facility of Switzerland – Emiko Uchikawa (Dubochet Center for Imaging (DCI), Lausanne)
11:30 – 12:00	Using Scipion in SBGrid – Estrella Fernández (SBGrid Consortium, Boston)
12:00 – 12:30	Coffee break
12:30 – 13:00	Cryo-EM in CNPEM – Rodrigo Villares Portugal (CNPEM, Campinas)
13:00 – 13:30	Advancing Cryo-EM Services at ESRF with Scipion – Isai Kandiah (ESRF, Grenoble)
13:30 – 14:00	Discussion and conclusions
14:00	Lunch

Registration will be free for all attendeess

Further details, such as class locations, meeting links, title updates, and instructions for reaching the centre, will be provided in the weeks leading up to the workshop.

Scipion for facilities: Practical Course and Workshop. November 5th – 7th, 2024

July, 2024March, 2025 by Oscar Saiz

Dates: November 5-7th 2024 (3 EU afternoons or 3 east US mornings)

Venue: Hybrid format

Aim: The aim of this meeting is to gather feedback and showcase how facilities are using Scipion, demonstrating its capabilities and benefits for Cryo-EM facilities. 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.

Conditions: The workshop will be held at the Spanish National Centre for Biotechnology in Madrid, Spain. For the practical session on November 5, in-person attendance is required, and you must select this option on the registration page to ensure we prepare a machine for you. The main workshop on November 6-7 can be attended either in person or remotely.
No programming skills are required. We will use in-house bigbluebutton conference system. Verify your browser works at https://demo.bigbluebutton.org/

Program:

We start at:
San Francisco – 05:00 // Minneapolis – 07:00 // New York – 08:00 // São Paulo – 09:00 // Madrid – 14:00 // London – 13:00
Beijing – 20:00 // Tokyo – 21:00 // Sydney – 23:00

PRACTICAL COURSE

Tuesday 5th November – In person

14:00 – 14:30     Course Overview – Pablo Conesa, Biocomputing Unit CNB – Madrid, Spain.
14:30 – 15:30     On-the-fly processing – Daniel Marchan, Biocomputing Unit CNB – Madrid, Spain.
15:30 – 16:00     Coffee break
16:00 – 17:00     Processing workflows and templates – Daniel Marchan, Biocomputing Unit CNB – Madrid, Spain.
17:00 – 17:45 Scipion with queue systems – Daniel Marchan, Biocomputing Unit CNB – Madrid, Spain.
17:45 – 18:30 Build your own workflow – Support from CNB staff

WORKSHOP

Wednesday 6th November – Hybrid

14:00 (CET) Welcome – Jose María Carazo , Biocomputing Unit CNB – Madrid, Spain.
14:15 – 14:45 An Overview of Scipion in Facilities – Pablo Conesa, Biocomputing Unit CNB – Madrid, Spain.
14:45 – 15:15 Automated on-the-fly data processing in EMhub is fantastic, but what’s next? – Jose Miguel de la Rosa Trevin, St Jude Children’s Research Hospital – Memphis, USA.
15:15 – 15:45 Lab Management with CEITEC: LIMS Demo and Key Features – Radek Veverka, Central European Institute of Technology at Masaryk University – Brno, Czech Republic.
15:45 – 16:15 Coffee break
16:15 – 16:45 Smart Data Collection with Smartscope – Jonathan Bouvette, Princeton University – New Jersey, USA.
16:45 – 17:15 Enhancing Smart Acquisition: Integrating SPA Processing Feedback with the Scipion-EM-SmartScope Plugin – Alberto Garcia, Biocomputing Unit CNB – Madrid, Spain.
17:15 – 18:00 Discussion and user input gathering

Thursday 7th November – Hybrid

14.00 (CET)      Enhancing Efficiency: Best Practices and Automations for On-the-Fly Processing in SPA Workflows – Daniel Marchan, Biocomputing Unit CNB – Madrid, Spain.
14:30 – 15:00     NextPyP: A scalable platform for single-particle cryo-EM/ET image analysis – Alberto Bartesaghi Duke University – Durham , USA.
15:00 – 15:30 Using Scipion to enable diverse cryo-ET workflows to explore Neurodegeneration at UCSF – Eric Tse, Institute for Neurodegenerative Diseases UCSF – San Francisco, USA.
15:30 – 16:00     Coffee break
16:00 – 16:30     Scipion use Case: Stream processing at CNB Facility – Javier Chichon, CryoEM Facility CNB – Madrid, Spain.
16:30 – 17:00     Expanding access to cryo-EM through specimen preparation robotics and platform-independent remote imaging – Mario Borgnia, National Institute of Environmental Health Sciences – Durham, USA
17:00 – 18:00     Discussion and conclusions

National Center for Biotechnology (CNB), Madrid, Spain
Madrid, November 5 – 7, 2024
How to find us: Contact Us – I2PC – Instruct Image Processing Center

REGISTRATION

Registration will be free for all attendees.
Fill your application here

Further details, such as class locations, meeting links, title updates, and instructions for reaching the centre, will be provided in the months leading up to the workshop.

Scipion at facilities workshop. October 17th & 18th, 2023

September, 2023February, 2026 by

Dates: 17th & 18th October 2023 ( 2 EU afternoons or 2 US ET mornings)
Venue: Remote (https://conectaha.csic.es/b/bla-i7j-g7z-klh)

Aim: The aim of this meeting is to get feedback and showcase how facilities are using Scipion and show what Scipion offers to a Cryo-em facility. There will be talks but also plenty of time for discussion.

Target Audience: Cryo-em facility staff wanting to do or already doing on-the-fly processing.

Conditions: The workshop will be remote. No programming skills are required. We will use in-house bigbluebutton conference system.
Verify your browser works at https://demo.bigbluebutton.org/

Program:

San Francisco – 05:00 // Minneapolis – 07:00 // New York – 08:00 // São Paulo – 09:00 // Madrid – 14:00 // London – 13:00
Beijing – 20:00 // Tokyo – 21:00 // Sydney – 23:00

Tuesday 17th October – New developments/Solutions

14.00 (CEST) Welcome – Jose María
14.15-14:40 Introduction to Scipion – Pablo Conesa (CNB)
14:40-15:20 Optimizing Cryo-EM facilities with SmartScope – Jonathan Bouvette (Princeton)
15:20-16:00 Scipion and Smart scope – Alberto García (CNB)
16:00-16:40 EMhub: a web platform for CryoEM centers management and on-the-fly data processing (Jose Miguel de la Rosa (St. Jude Children’s Research Hospital Memphis, TN, USA)
17:20-18:00 Streaming and Unattended Workflows for SPA Processing – Daniel Marchan (CNB)

Wednesday 18th October – Facilities real cases

14.00 (CEST) Data flow in cryo-EM facilities: LMB example – Grigory Sharov (LMB)
14.15-14:40 CM01 and processing pipeline at ESRF – Isai and Olof (ESRF)
14:40-15:20 Setup at CNB – Javier Chichón (CNB)
15:20-16:00 Facilities + Tomography + Scipion – Pablo Conesa (CNB)
16:00-17:45 Discussion and conclusions
– Data storage and transfer
– IT support
– Reporting
– Automation: Grid screening, acquisition image processing
– Others?
17:45-18.00 “Group picture” + End

National Center for Biotechnology (CNB), Madrid, Spain
Madrid, October 17 – 18, 2023
How to find us: https://idospece.i2pc.margaro.eus/contact-us/

REGISTRATION

Registration will be free for all attendees.
Fill your application here

Scipion at facilities workshop. October 4th, 2022

July, 2022February, 2026 by

Dates: 4th October 2022
Venue: Hybrid Meeting (Brno/Remote)
The face-to-face meeting will take place at the CEITEC facilities (Kamenice 753/5, Brno, 625 00).
CEITEC Website: https://www.ceitec.eu/

Aim : The aim of this meeting is to mainly get feedback and showcase how facilities are using Scipion and show what scipion offers to a Cryo-em facility. There will be talks but also plenty of time for discussion.

Target Audience: Cryo em facility staff wanting to do or already doing on-the-fly processing.

Conditions: The workshop will be hybrid: online and presential (in Brno) for both attendees and speakers.
No programming skills are required.

Program: This program is tentative and may be subjected to changes depending on the attendees. Anyone is welcome to present their infrastructure.

9.00 Welcome
9.15 Brief update on Scipion for facilities CNB
9.45-13.00 Examples of setup, use, hardware and software architecture: ESRF, CNB, Francis Crick, SciLife Lab, NIEHS, UCSF (there will be a 20 minutes break)
13.00 Lunch
14.00 Discussion: Usability, maintainability, IT support, needs, reporting.
16.00 Brainstorming
16.45 Conclusions
17.00 End

REGISTRATION

Registration will be free for all attendees.
Fill your application here.

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Workshop on Algorithms for 3D Reconstruction in Soft X-Ray Microscopy. Madrid, January 20th-21st

May, 2014March, 2025 by admin

An intensive meeting devoted to discuss the image processing challenges raised by recent advances in Soft X-ray tomography of cellular materials at cryogenic temperatures. The topics to be discussed include Image Formation, Depth of Field and Zone Plates, Contrast Enhancement, information Recovery and Tomographic Algorithms.

I2PC Developer Workshop

January, 2012March, 2025 by admin

The first I2PC Developer Workshop will take place in Madrid, 6th and 7th of February. The main objective is to standardize information exchange in Single Particles as well as to start a dynamic of algorithm benchmarking in the field. Concrete conclussions on data interchange were reached and a first benchmarking challenge was issued to the community.

Jose Maria Carazo: Introduction and setting the goals and expectation of this meeting.

Cryo-EM Facilities Meeting 2026

Aim

Conditions

Program

Program:

We start the day at:

AGENDA

Program:

We start at:San Francisco – 05:00 // Minneapolis – 07:00 // New York – 08:00 // São Paulo – 09:00 // Madrid – 14:00 // London – 13:00Beijing – 20:00 // Tokyo – 21:00 // Sydney – 23:00

PRACTICAL COURSE

Tuesday 5th November – In person

WORKSHOP

Wednesday 6th November – Hybrid

Thursday 7th November – Hybrid

Program:

San Francisco – 05:00 // Minneapolis – 07:00 // New York – 08:00 // São Paulo – 09:00 // Madrid – 14:00 // London – 13:00Beijing – 20:00 // Tokyo – 21:00 // Sydney – 23:00

Tuesday 17th October – New developments/Solutions

Wednesday 18th October – Facilities real cases

Benchmarks

Workflows in Single Particle

Ontologies and Vocabularies

We start at:
San Francisco – 05:00 // Minneapolis – 07:00 // New York – 08:00 // São Paulo – 09:00 // Madrid – 14:00 // London – 13:00
Beijing – 20:00 // Tokyo – 21:00 // Sydney – 23:00

San Francisco – 05:00 // Minneapolis – 07:00 // New York – 08:00 // São Paulo – 09:00 // Madrid – 14:00 // London – 13:00
Beijing – 20:00 // Tokyo – 21:00 // Sydney – 23:00