Program
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: Spatial Omics analysis of colorectal malignancy transformation from cell to tissue scale
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 and Nour Bazzi: Experimental design for combining modalities in spatial transcriptomics
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 – Speaker TBD: 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 and SpaceTrooper: unified infrastructure and quality control workflows for spatial omics data
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: Slide-Seq: From Sample Preparation to Spatial Transcriptome Analysis
15:45 – 18:45
Workshop Session C
WS 5: Sergio Salas: Segmentation strategies for accurate transcript-cell assignment in image-based spatial transcriptomics data
20:30 – 22:00
Lecture 8 - Marcelo Nollman: Spatial genomics by chromatin tracing: linking transcription to 3D genome organization
Thursday, September 17th
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
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 6: Laura Cantini: STORIES: Cell trajectory inference in spatial transcriptomics
WS 7: Hugo Blanc: From Pixels to RNAs: a hands-on MERFISH image-processing workshop
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