First Spatial-Cell-ID Summer School

SCID 2026 is built around collaborative learning. Our “Round Table with Experts / Q&A / Bring Your Own Data” sessions are your chance to share your own data with bioinformatician with extensive experience in spatial transcriptomics. These sessions are designed for open discussion, where you can get feedback, troubleshoot analysis errors, and solve the practical problems of spatial transcriptomics data analysis.

Summer School Program

Sunday, September 13th

16:00 – 18:45
Participant’s arrival
18:45 – 19:50
Dinner
19:50 – 20:00
Welcome and General Introduction
20:00 – 21:30
Lecture 1 – Anna Pascual: Title TBD
21:30 – 00:00
Drinks

Monday, September 14th

07:30 – 08:45
Breakfast
08:45 – 10:15
Lecture 2 – Sophie Pantalacci: Challenges of annotating and comparing scRNAseq datasets in a spatio-temporal context
10:15 – 10:45
Coffee Break
10:45 – 12:15
Lecture 3 – Ahilya Sawh: Chromosome acrobatics during development
12:15 – 14:00
Lunch
14:00 – 15:30
Round Table with Experts / Q&A / Bring Your Own Data
15:45 – 18:45
Workshop Session A (Parallel)
WS 1: Quentin Blampey: Deep learning and computational methods for spatial data analysis
WS 2: Jennifer Love: Combining RNA and DNA FISH: a case study
19:30 – 20:30
Dinner
20:30 – 22:30
Poster Session I & Participant Flash Talks

Tuesday, September 15th

08:45 – 10:15
Lecture 4 – Hilde Nelissen: Linking Spatial Context to Cell Fate: Trajectories in the Maize Shoot Apical Meristem
10:45 – 12:15
Lecture 5 – Jonathan Enriquez: Title TBD
15:45 – 18:45
Workshop Session B (Parallel)
WS 3: Nadav Yayon: Harnessing morphological information for spatial biology analysis
WS 4: Dario Righelli: SpatialExperiment: infrastructure in R using Bioconductor
20:30 – 22:30
Poster Session II & Participant Flash Talks

Wednesday, September 16th

08:45 – 10:15
Lecture 6 – Yad Ghavi Helm: From single-cell to spatial transcriptomics: reconstructing gene expression and enhancer activity in a developing embryo
10:45 – 12:15
Lecture 7 – Nathalie Beaujean: Title TBD
15:45 – 18:45
Workshop Session C (Parallel)
WS 5: Helena Cornwell: Title TBD
WS 6: Sergio Salas: Segmentation strategies for accurate transcript-cell assignment in image-based spatial transcriptomics data
20:30 – 22:00
Lecture 8 - Marcelo Nollman: Title TBD

Thursday, September 17th

08:45 – 10:15
Lecture 9 – Zayna Chaker: Title TBD
10:45 – 12:15
Lecture 10 – Laura Cantini: Multi-modal learning for single-cell data integration
15:45 – 18:45
Workshop Session D (Parallel)
WS 7: Laura Cantini: STORIES: Cell trajectory inference in spatial transcriptomics
WS 8: Hugo Blanc: Title TBD
19:30 – 00:00
Gala Dinner and Party

Friday, September 18th

08:45 – 10:15
Lecture 11 – Thomas Walter: Title TBD
10:45 – 12:15
Lecture 12 – Teva Vernoux: Title TBD
12:15 – 13:30
Lunch and departure