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
19:00 – 19:50
Dinner
19:50 – 20:00
Welcome and General Introduction
20:00 – 00:00
Drinks and get to know each other

Monday, September 14th

07:30 – 08:45
Breakfast
08:45 – 10:15
Lecture 1 – Yad Ghavi-Helm: From single-cell to spatial transcriptomics: reconstructing gene expression and enhancer activity in a developing embryo (salle Parrachée)
10:15 – 10:45
Coffee Break
10:45 – 12:15
Lecture 2 – Nathalie Beaujean: Slide-Seq: From Sample Preparation to Spatial Transcriptome Analysis (salle Parrachée)
12:15 – 13:30
Lunch
13:30 – 15:15
Round Table with Experts / Q&A / Bring Your Own Data (mezzanine et bar)
15:15 – 15:45
Coffee Break
15:45 – 18:45
Workshop Session A
WS 1: Quentin Blampey: Deep learning and computational methods for spatial data analysis (salle Scolette)
19:30 – 20:30
Dinner
20:30 – 22:30
Poster Session I & Participant Flash Talks (mezzanine et salle Parrachée)

Tuesday, September 15th

07:30 – 08:45
Breakfast
08:45 – 10:15
Lecture 3 – Hilde Nelissen: Linking Spatial Context to Cell Fate: Trajectories in the Maize Shoot Apical Meristem (salle Parrachée)
10:15 – 10:45
Coffee Break
10:45 – 12:15
Lecture 4 – Yinan Wan: Whole-embryo spatiotemporal transcriptomics at subcellular resolution (salle Parrachée)
12:15 – 13:30
Lunch
13:30 – 15:15
Round Table with Experts / Q&A / Bring Your Own Data (mezzanine et bar)
15:15 – 15:45
Coffee Break
15:45 – 18:45
Workshop Session B (Parallel)
WS 2: Nadav Yayon: Harnessing morphological information for spatial biology analysis (salle Scolette)
WS 3: Dario Righelli: SpatialExperiment and SpaceTrooper: unified infrastructure and quality control workflows for spatial omics data (salle Norma)
19:30 – 20:30
Dinner
20:30 – 22:30
Poster Session II & Participant Flash Talks (mezzanine et salle Parrachée)

Wednesday, September 16th

07:30 – 08:45
Breakfast
08:45 – 10:15
Lecture 5 – Thomas Walter: Computational Methods for Linking Morphological Phenotypes and Spatial Gene Expression (salle Parrachée)
10:15 – 10:45
Coffee Break
10:45 – 12:15
Lecture 6 – Ahilya Sawh: Chromosome acrobatics during development (salle Parrachée)
12:15 – 13:30
Lunch
13:30 – 15:15
Round Table with Experts / Q&A / Bring Your Own Data (mezzanine et bar)
15:15 – 15:45
Coffee Break
15:45 – 18:45
Workshop Session C (Parallel)
WS 4: Arne Defauw: Scalable and Interactive Spatial Omics Analysis with Harpy (salle Scolette)
WS 5: Jennifer Love and Nour Bazzi: Experimental design for combining modalities in spatial transcriptomics (salle Norma)
19:30 – 20:30
Dinner
20:30 – 22:30
Poster Session III & Participant Flash Talks (mezzanine et salle Parrachée)

Thursday, September 17th

07:30 – 08:45
Breakfast
08:45 – 10:15
Lecture 7 – Sophie Pantalacci: Challenges of annotating and comparing scRNAseq datasets in a spatio-temporal context (salle Parrachée)
10:15 – 10:45
Coffee Break
10:45 – 12:15
Lecture 8 – Laura Cantini: Multi-modal learning for single-cell data integration (salle Parrachée)
12:15 – 13:30
Lunch
13:30 – 15:15
Round Table with Experts / Q&A / Bring Your Own Data (mezzanine et bar)
15:15 – 15:45
Coffee Break
15:45 – 18:45
Workshop Session D
WS 6: Laura Cantini and Anthony Ozier-Lafontaine: Biologically interpretable spatial domain identification in spatial transcriptomics data (salle Scolette)
19:00 – 01:00
Gala Dinner and Party

Friday, September 18th

07:30 – 08:45
Breakfast
08:45 – 10:15
Lecture 9 – Zayna Chaker: Reshuffling the cards: Spatial transcriptomics reveal a novel compartmentalisation of adult brain stem cell niches during pregnancy (salle Parrachée)
10:15 – 10:45
Coffee Break
10:45 – 12:15
Lecture 10 – Marcelo Nollman: Spatial genomics by chromatin tracing: linking transcription to 3D genome organization (salle Parrachée)
12:15 – 12:30
Concluding remarks
12:30 – 13:00
Packed lunch and departure