This hackathon will take place from Monday 9th Dec - Wednesday 11th Dec 2024. The timing of this event will be Central European Time (CET). The event precedes the European Society for Spatial Biology’s inaugural conference on 12-13 Dec.

>> Join via Teams <<

Day 1: Monday 9th December 2024 [Times in CET]

09:30-10:00 Arrival and coffee - Esther Lederberg conference room, floor 2 room 328
10:00-10:30 Welcome and introduction SpaceHack drawing, Naveed Ishaque, Berin Institute of Health
10:30-11:00 SpaceHack Cloud and GitHub drawing, Sven Twardziok and Naveed Ishaque, Berin Institute of Health
11:00-11:15 Cell segmentation from commercial platforms - the past, present & future drawing, Thomas Conrad, Berin Institute of Health
11:15-11:30 10X Genomics - tech, data, project pitch drawing, Patrik Roelli, 10x Genomics
11:30-11:45 Vizgen - tech, data, project pitch drawing, Dries Vanhemelen, Vizgen
11:45-12:00 Nanostring/Bruker - tech, data, project pitch drawing, Christoph Koenig, Nanostring/Bruker
12:00-13:00 Lunch
13:00-13:30 Stand up and pitch your projects

  • Project 1 - BioImageArchive spatial transcriptomics data deposition guide drawing, Teresa Zulueta-Coarasa
  • Project 2 - FspQC drawing, Florian Heyl
  • Project 3 - A Hitchhiker’s guide to a spatial data analysis drawing, Sara Jimenez, Francesca Drummer
  • Project 4 - SpacePerturb drawing, George Gavriilidis
  • Project 5 - PASTA: a guide for spatial statistics application to spatial transcriptomics, Samuel Gunz, Martin Emons
  • Project 6 - SEGGER - delving into the dark side of cell segmentation drawing, Elyas Heidari
  • Project 7 - SpatialLeiden v2 - adding multi-omics and multi-sample support drawing, Niklas Boetticher and Paul Kiessling
  • Project 8 - SpaceCompare drawing, Brian Long
  • Project 9 - MolKart, a NF-CORE workflow for im-SRT drawing, Sebastian Gonzalez-Tirado, Migueal A Ibarra-Arellano

13:30-14:30 Match making - join project teams and start hacking
14:30-15:00 Coffee/tea break
15:00-17:15 Hacking!
17:15-17:30 SpatialCompare - A QC tool for investiating uniformity of gene expression over tissues drawing, Brian Long, Allen Inst for Brain Science
17:30-18:00 USA alignment - quick overview of GitHub, Cloud, and projects
18:00-18:15 Talk - The European Society for Spatial Biology drawing, Denis Schapiro, Heidelberg University Hospital
18:15-20:00 sponsored activity: Berlin Computer Game Museum with guided tour. Karl-Marx-Allee 93a, 10243 Berlin.
21:00-23:00 sponsored dinner: Vesuvio Trattoria. Strausberger Pl. 8, 10243 Berlin. 2 course menu. Choice of 6 dishes. 3 drinks included.

Day 2: Tuesday 10th December 2024

09:00-09:30 Alignment with Australia + project recap
09:30-10:00 The EBI BioImage Archive for Spatial Transcriptomics drawing, Teresa Zulueta-Coarasa, EBI BioImage Archive
10:00-12:00 Hacking (inc coffee break)
12:00-13:00 Lunch
13:00-13:15 Group photo
13:15-15:30 Hacking
15:30-16:00 Break
16:00-17:30 Hacking
17:30-18:00 Alignment with USA
18:00-20:00 Optional evening activity: Medieval Christmas Market at the RAW

Day 3: Wednesday 11th December 2024

09:00-09:30 Alignment with Australia + project recap
09:30-12:00 Hacking (inc coffee break)
12:00-13:00 Lunch
13:00-15:00 Project wrap up, presentation preparation, BioHackRxiv-ing
15:00-15:30 Break
15:30-17:00 Presentation from team leads

  • Project 1 - BioImageArchive spatial transcriptomics data deposition guide, Teresa Zulueta-Coarasa
  • Project 2 - SpatialCompare, Brian Long, Florian Heyl
  • Project 3 - A Hitchhiker’s guide to a spatial data analysis, Sara Jimenez, Francesca Drummer
  • Project 4 - SpacePerturb, George Gavriilidis
  • Project 5 - PASTA: a guide for spatial statistics application to spatial transcriptomics, Samuel Gunz, Martin Emons
  • Project 6 - SEGGER - delving into the dark side of cell segmentation, Elyas Heidari
  • Project 7 - SpatialLeiden v2 - adding multi-omics and multi-sample support, Niklas Boetticher and Paul Kiessling

17:00-18:00 Alignment with USA