VIB Hackathon June 2024 on spatial omics

Last updated: 31th of May 2024

Three-day hackathon for spatial omics tools and methods

For the hackathon results, see the code repo and preprint:

During a three-day hackathon, work was performed on various topics within the field of spatial omics data analysis. The topics were organized in five workgroups and included benchmarking, pipelines, spatial transcriptomics, spatial proteomics, spatial multi-omics and cell-cell communication. Most tools and methods were considered in the context of the Python ecosystem for spatial (SpatialData) and single-cell (scverse) data analysis.

Rombaut, Benjamin, Lotte Pollaris, Chananchida Sang-aram, Michiel V. Cruysse, Robrecht Cannoodt, Frank Vernaillen, Arne Defauw, et al. 2024. “VIB Hackathon on Spatial Omics Tools and Methods.” BioHackrXiv. June 25. doi:10.37044/osf.io/uf7d3.

Monday 10th until Wednesday 12th June 2024
Seminar room L5, VIB-UGent Center for Medical Biotechnology
Technologiepark-Zwijnaarde 75, Ghent, Belgium

Enter the CMB entrance and go to the fifth floor via the stairs or elevator.

We're happy to have participants of over 30 institutes in 12 countries
The application deadline has passed and the form is closed, but all hackathon materials will be announced and made available here. Info on the previous hackathon in September 2023.

Organised by the Saeys Lab at VIB-UGent Center for Inflammation Research.
Sponsored by the VIB Spatial Catalyst, VIB.AI and Data Intuitive.
For questions, send a message via the Zulip stream or email to [e-mail].

It is highly recommended but not mandatory to attend the VIB Spatial Omics conference also in Ghent afterwards on 13-14 June. For info and registration: https://www.vibconferences.be/events/spatial-omics.

Important dates:

• 8th March 2024 Hackathon application form closes
• 15th March 2024 Hackathon selection announcement
• 21th March 2024 Conference travel grant deadline
• 18th April 2024 Conference abstract deadline
• 2nd May 2024 Conference early bird deadline
• 10st May 2024 Waitlist announcement at the latest
• 30th May 2024 Conference final registration deadline
• 10th June 2024 Start of Hackathon

Quick links to:

• Main communication channel: image.sc Zulip stream
• Repository for shared code: saeyslab/VIB_Hackathon_June_2024
• Hackathon slidedeck: Slide deck
• Tracker of all hackathon code issues: GitHub Issues Kanban board

Objectives

Hackathon for spatial omics tools and methods

• Find synergies and foster collaborations in an open setting
• Share open-source code and slides
• Document and improve interoperability between new and existing tools and frameworks

5 Workgroups

1. Benchmarking and high-performance computing

• Spatial challenges for OpenProblems
• Nextflow, Dask Diagnostics, Hydra, Slurm jobs

2. Frameworks and interoperability

• Zarr, OME-NGFF, SpatialData
• Reading/writing using S3 remote storage and MinIO
• squidpy, MCMICRO, napari

3. Spatial single-cell technologies

• transcriptomics: 10x Visium HD, Vizgen MERSCOPE, 10x Xenium, Resolve MC
• proteomics: Miltenyi MACSima, Akoya Phenocycler

4. Spatial multi-omics

• Multimodal data integration methods

5. Downstream analysis

• niche detection methods
• cell-cell communication methods

Suggest additional working groups and topics using the application form

Given the popularity of the programming language in the field, most of the work will be in Python. There is however also interest for interoperability with R (e.g. SpatialData in R, Giotto Suite) and JavaScript (e.g. vitessce).
Bring your own laptop and headphones. Additional computational resources are available for all hackathon participants (Tier1 HPC access by VSC, S3 object storage by VIB Data Core).

Hackathon program

Mon 10th June

13:00-13:30 Registration
13:30-14:00 Welcome and introduction
14:00-15:00 Setup, get to know your workgroup and task divisions
15:00-15:30 Quick rundown of work items per group
15:30-16:30 Hacking
16:30-16:45 Update progress slides
16:45-17:00 Status updates from participants

18:30 Dinner and drinks
Belgian dishes @ Multa Tuli
Huidevetterskaai 40, 9000 Gent

Tue 11th June

9:00-11:15 Hacking
11:15-11:30 Update slides with progress
11:30-12:00 Report on progress and issues
12:00-13:00 Lunch
13:00-16:00 Hacking
16:00-16:15 Group picture and break
16:15-18:00 Hacking

18:00 Dinner and drinks
Pizza and Belgian beers/beverages on-site

Wed 12th June

9:00-11:15 Hacking
11:15-11:30 Update slides with progress
11:30-12:00 Report on progress and issues
12:00-13:00 Lunch
13:00-16:00 Hacking
16:00-17:00 Finish up final notes, issues and future work

Thu 13th - Fri 14th June

VIB Conference on Spatial Omics in Ghent
https://www.vibconferences.be/events/spatial-omics

Travel details

• Participation is free, but registration is mandatory and seats are limited.
• Thanks to our co-organisers and sponsors, we can provide free coffee and beverages throughout the hackathon. A nice lunch will be provided for you on Tuesday and Wednesday, with vegetarian and vegan options. The first night we will organise a dinner in the city center. The second night we will provide (meat and vegan) pizzas on-site,
• The conference location De Bijloke is also near station Gent-Sint-Pieters (15min walking distance)
• Public transport with De Lijn is available between Gent-Sint-Pieters railway station and Tech Lane Park (15 min with bus 50 or 70 from terminal 6 or 7 or with tram T3 stop Klaartestraat and 7 min walk).
• Paying on the bus by card or with the app for one ticket is 2,5 euros. It's 1,7 euro if you get 10 tickets.
• You can alternatively rent a Donkey Republic bike for 3 days or a week.
• If you want to travel by car, there is parking available at the hackathon venue. Parking is free and the barrier opens automatically if you send us your license plate number by the 25th of May. The venue is accessible by car, but note that cars have limited access to the city center.
• For activities and accommodation in Ghent, check out visit.gent.be and vibconferences.be/host-city-ghent. Feel free to contact us with specific travel questions.