2nd ETSI Hackathon, November 3-4, 2024, Tampa, FL, USA

Welcome to the official page of the 2nd ETSI Hackathon!

Organizers: The 2nd hackathon event of the Emission Tomography Standardization Initiative (ETSI) is organized by the ETSI Consortium Leadership Team and is officially supported by:

Location: The event will take place at Tampa, FL, USA at the Hilton Embassy Suites Downtown Tampa hotel (Gandy Meeting Room on the 2nd floor) located close to the Tampa Convention Center. Room Rate is $229 per night + tax and must be booked by October 3, 2024 (please use registration link below to book your room, for those attending the IEEE NSS/MIC conference and plan to stay at the same hotel please note that a separate booking must be made for each event)!

Time: November 3-4, 2024 (Sunday & Monday right after 2024 IEEE NSS/MIC)

Registration: The event is free to attend in-person or remotely, however registration is required. Please register in the link below:

Registration

Pre-registration is no longer required. Thank you for submitting your pre-registration information.

Overview

The 2nd hackathon event of the Emission Tomography Standardization Initiative (ETSI) will be held on November 3-4, 2024, in Tampa, FL, USA, right after the IEEE Nuclear Science Symposium and Medical Imaging Conference also taking place in Tampa a few days earlier (October 26 -November 2, 2024) .

The time and location were chosen to facilitate participation of attendees of the IEEE NSS/MIC meeting with an interest in the standardization of emission tomography raw data. An active community of developers has already been created since last year (1st ETSI Hackathon Developers Team) and we are very much looking forward to new members joining this team in this year’s hackathon to work all of us together for the next geenration of nuclear medical imaging raw data standards as part of ETSI’s mission!

Sponsorship: We highly welcome previous and new sponsors to support this year’s ETSI hackathon. Any interested sponsor is welcomed to directly contact for details Kris Thielemans and Nicolas Karakatsanis. We will begin announcing sponsors soon.

This page will be regularly updated with more details about the registration, the sponsorships and the program of the hackathon in the following weeks. If you would like further information about ETSI’s 2nd Hackathon, please consider subscribing to ETSInitiative.org for automated updates and/or directly contact Kris Thielemans or Nicolas Karakatsanis.

Objectives

This event will focus again this year on ETSI’s PETSIRD standardized format for PET raw data. The primary objectives of the 2nd ETSI hackathon event is to demonstrate in-silico end-to-end proof of principle application of the PETSIRD format. For this purpose we aim at:

  • continuing raising awareness and educating the nuclear medical imaging sciences field regarding the need for raw emission data standardization
  • growing the momentum for defining usable raw emission data standards as built from last year’s 1st ETSI hackathon and its recently formed ETSI developers’ community,
  • updating on the latest data elements and features of the PET ETSI raw data (PETSIRD) and discussing future directions and priorities for ETSI data standards, as well as
  • advancing and expanding on the set of characteristic use cases developed and demonstrated during last year’s 1st ESTI hackathon, including validated code libraries supported by the latest Yardl code building library.

The produced use-cases may constitute a basis for later developing respective use-cases for other types of emission tomography such as SPECT and planar imaging raw data standards.

Potential Use-Cases

We intend to mainly update the use-cases developed in the previous ETSI hackathon, taking changes in the proposed standard into account, and exploiting new functionality. However, participants are very welcome to suggest other use-cases before or during the hackathon. Potential use-cases include: 

  • Update Monte Carlo GATE ROOT-to-PETSIRD data format convertor 
  • Update analytic simulation use-case to generate PETSIRD data 
  • Visualization of scanner geometry and example LORs 
  • Integrate PETSIRD format into open-source reconstruction packages taking updated geometry and normalization definitions into account
  • Update list-mode manipulation use-case (splitting, merging etc.) 
  • Gated image reconstruction 
  • Data-driven motion signal extraction  

Use-Cases GitHub Repository

In the ETSIhacker’s GitHub public repository we share a set of software tools developed during our 2nd hackathon demonstrating a set of expanded practical use-cases for the data standard since the previous hackathon, including

  • update of convertors from simulated or real list-mode data into the latest standard format (e.g. from Monte-Carlo simulations or vendor scanners)
  • expansion of the list of basic list-mode data operations (e.g. subsampling, gating etc.),
  • upgrading of user-friendly interfaces linking the data standards with existing open-source image reconstruction software (e.g. CASToR, PyTomography, STIR etc.), and
  • visualization of the scanner geometry description embedded in the data standard

Hackathon Program

Start: sUNDAY November 3rd @07:45
End: monday november 4th @16:30

Sunday Morning: 07:45-12:30

  • Meet & Greet light Breakfast (07:45)
  • ETSI’s mission and the PETSIRD raw data format (08:30) – Nicolas Karakatsanis & Adam Kesner
  • Yardl overview & updates (08:50) – John Stairs/Joseph Naegele
  • Updates on PETSIRD definitions (09:15) – Kris Thielemans
  • Intro on PET data “Normalization” (09:45) – Kris Thielemans
  • Existing Use Cases (10:00) – Nicolas Karakatsanis
  • Coffee Break (10:30)
  • Organization into Developer Subgroups (10:45) – Glenn Wells

Sunday Lunch (12:30-13:30)

  • Group lunch (on-site) (12:30)

Sunday Afternoon (13:30-17:30)

  • Developer Subgroups formation (13:30)
  • Software set-up (hands-on) (13:45)
  • Work in subgroups (14:00)
  • Coffee/Tea Break (15:30)
  • Work in subgroups (15:45)
  • Progress report after first day (17:15)

Sunday Evening (17:30-20:00) 

  • Hackathon Group dinner (on-site, 17:30)

Monday Morning (09:00-12:30)

  1. Light breakfast (08:30)
  2. Recap of previous day activities (09:00)
  3. Work in subgroups (09:15)
  4. Coffee/Tea Break (10:45)
  5. Work in Subgroups (11:00)
  6. Subgroups Progress Report (12:15)

Monday Lunch (12:30-13:30)

  • Group lunch (on-site, 12:30)

Monday Afternoon (13:30-16:30)

  1. Work in subgroups (13:30)
  2. Coffee/Tea Break (15:30)
  3. Final progress report (15:45)
  4. Next steps and conclusion of the hackathon (16:00)
  5. End of event & farewell (16:15)

Monday Evening (16:30-18:30)

  • Group dinner (optional, off-site, 16:30)

Important Information for Registered Attendees

On-site (in-person) attendees

Location: Embassy Suites Downtown Tampa Hotel

  • The hotel is located very close (within 5-min walking distance) from the Tampa Convention Center where IEEE NSS/MIC will be held.
  • Please arrive on Sunday between 8:30 and 9:00am. There will be a light breakfast.
  • If you have registered to attend in-person but could not make it, you need to let us know ASAP.
  • If your dinner plans change, we need to know 4 days before the meeting.
  • Don’t forget to bring your laptop, charger and lots of enthusiasm!
  • More info will be available as we approach the event date. Stay tuned!

All (both on-site and on-line) attendees

We strongly advise to create a free GitHub account if you don’t have one yet. See Signing up for a new GitHub account – GitHub Docs.  You will need to have this to use GitHub Codespaces for cloud access. (Advanced users can of course install software on their own machine).

  • Note: if you’re a student or academic staff, you can apply for GitHub Education, which gives you some extra features, but this will not be required for this hackathon.

Discord platform was proven to be very useful last year for the efficient collaboration within and across the different subgroups during and after the 1st hackathon. We will therefore use the same Discord server that was originally set-up for the 1st ETSI hackathon to prepare for, collaborate during and follow-up after this hackathon event. This will allow seamless continuation of the discussions between the developer sub-groups, as initiated from last year. Please join our Discord server, if you have not done so, and start discussing with your peers and subgroup leaders about potential use cases you would like to work on during the 2nd ETSI hackathon.

PETSIRD Standard

The following major release (v. 0.2.0) of ETSI’s PETSIRD standard for PET list-mode data will be used as base reference in the 2nd ETSI Hackathon featuring:

  • major updates to the model: coincidence and triple events, scanner geometry, detection efficiencies and external signals. These are the result of discussions within the Data Elements (core members) sub-group of the ETSI Consortium.
  • auto-deployment to PyPI, i.e. pip install petsird.
  • updates to some support software, including yardl and conda

Data Repositories

Below you may find the published Zenodo repositories for the Monte Carlo (GATE) data built for the 2nd ETSI Hackathon use cases:

  • GATE simulation data (ROOT format) of a 3min PET scan of a modified NEMA IEC phantom filled with 18F radioactive water solution acquired with “ETSIPETscanner” model (520mm TFOV, 128mm AFOV): https://doi.org/10.5281/zenodo.13941538
  • GATE simulation data (ROOT format) of a 6min PET scan of a moving (1cm translation across all three Cartesian directions occurring at the start of the 3rd min of acquisition) voxelized brain Hoffman phantom with a 18F e+ source distribution acquired with “ETSIPETscanner2” model with a bit more extended AFOV to include the entire brain Hoffman phantom (520mm TFOV, 256mm AFOV)  https://doi.org/10.5281/zenodo.13963697

One of the use-cases during the hackathon will be to develop a convertor from ROOT format to our newly updated PETSIRD format definition and the subsequent production of PETSIRD demo list-mode data reflecting the above simulation cases to allow testing of some of our developed use-cases.

Hybrid meeting invitations

You will receive several Teams meeting invitations few days prior to the event. This will be most useful for online attendees of course. In addition, we will share the recordings occasionally via email.

  • We will make every effort to have the recordings of the 1st day sessions available several hours before the 2nd day sessions begin in order to facilitate their offline access for remote attendees in different time zones

We are very much looking forward to this meeting, and hope you are too!