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⬤ 9-11 December 2024 ⬤ Main location: Berlin ⬤ Satallite location: Memphis ⬤ Hybrid ⬤

>> Registration is now closed<<

SpaceHack is now an official a BioHackathon Germany event!

Abstract

Spatially resolved transcriptomics allows us to resolve gene expression in the native tissue context. Imaging-based spatial transcriptomics methods offer an unrivaled spatial resolution, however clear and agreed-upon data processing and analysis guides are lacking or fragmented. SpaceHack 3.0 aims to investigate and improve on the currently available information to help users make sense of their valuable data. We will focus on imaging-based spatial transcriptomics methods such as MERFISH, ISS, osmFiSH, STARmap, etc (not Visium, GeoMX, slide-seq, stereoseq, ...).

Project focus

The focus of our BioHackathon project will be on investigating, reporting, and improving user guides for imaging-based spatial transcriptomics. The format will be a hackathon with a "bring your own project" setup. Not everyone needs to propose a project, but here are some projects that some people will be bringing with them:

  1. BioImageArchive spatial transcriptomics data deposition guide (Teresa Zulueta-Coarasa, EBI/UK)
  2. Spatial QC - gene expression uniformity over tissue (Brian Long, Allen Brain Isnt/USE)
  3. A Hitchhiker’s guide to a spatial data analysis (Sara Jimenez and Francesca Drummer, Munich/DE)
  4. Effect of segmentation & pre-processing on spatial perturbation modelling (George Gavriliidis, CERTH/GR)
  5. PASTA - a guide for spatial statistics application to spatial transcriptomics (Samuel Gunz and Martin Emons, UZH/CH)
  6. SEGGER - delving into the dark side of cell segmentation (Elias Hydari, Heidelberg/DE)
  7. SpatialLeiden v2 - adding multi-omics and multi-sample support (Niklas Boetticher and Paul Kiessling, BIH/DE, Aachen/DE)

While the primary aim of the project will be to have fun and meet other spatial researchers, we will endeavor to disseminate our findings. This year we plan to wrap up our progress into a BioHackRxiv white paper.

Organisational details

Target audience: PhD/postdoc-level bioinformaticians familiar with spatial omics analysis. We would strongly encourage those with prior experience in spatial data analysis to apply! This will not be a tutorial, so be ready to contribute ;p.

Dates: Monday 9th - Wednesday 11th December 2024. The event precedes the European Society for Spatial Biology's inaugural conference on 12-13 Dec.

Location: Rahel Hirsch Center, 65 Luissenstrasse, 10117 Berlin, Germany. The venue for the SpaceHack is located in the Rahel Hirsch Center (Berlin Institute of Health) right next to the main Charite Hospital building.

Transport: GoogleMaps offers very reasonable suggestions in Berlin. Some suggestions:

  • Airport: BER Berlin Brandenburg Aiport. There are trains (FEX/RE8/RB23/...) going to Berlin Hauptbahnhof (Berlin Central Station) every 20 minutes. Tickets can be downloaded via the BVG app and cost ~3-4 Euro for a Berlin ABC ticket.
  • Train station: Berlin Hauptbahnhof (Berlin Central Station) and walk for 12 minutes, or take the tram M5/M8/M10 to "Invalidenpark"

Contact: for more information email Naveed Ishaque, [email protected]

Registration is now closed

Costs: registration for the hackathon is free, however, you will have to pay your own travel, food and accommodation expenses. We will cover lunch and drinks during the event.

Accommodation: please check the usual hotel booking portals. AO Hostels is a cheap option closeby, but there are many options in the vicinity.

Organizing committee:

  1. Main event, Berlin and online: Naveed Ishaque, Berlin Institute of Health at the Charité, Germany. Naveed leads a bioinformatics research group with a strong focus on developing and applying computation methods to better understand spatially resolved transcriptomics data.
  2. Memphis: Jasmine Plummer. Website. Address: MS 322, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105-3678 USA

Sonsors: We are proud to say that 10x and Vizgen are all contributing data, personnel and financial support to SpaceHack 3.0! We also thank the German Federal Ministry for Education and Research (FKZ:031L0265).

Code of Conduct

We want the hackathon to be fun, safe and inclusive. Participants are expected to adhere to the de.NBI Code Of Conduct and the BIH DEI statement.

We will continue to update this website until the start of the hackathon.

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