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The spatio-temporal transcriptome of single cells in their tissue

Presentation

Goal ? A national equipment to identify and characterize the transcriptome of each cell, while keeping its spatial position, in multicellular organisms

Where ? In Lyon, France

How ? Latest developments in spatial transcriptomics, some of which are not commercialized yet, for small to large numbers of transcripts, in intact or sorted cells, in whole organisms or tissue sections, combined with data analysis.

Approaches

Slide-seq
Slide-seq: Optimal tool to quantify the expression pattern of a large number of transcripts (~5000) with a high spatial resolution (3-10 μm) on tissue sections.
Spatial scRNAseq
Optimized tool for transcriptome analysis of a large number of individual cells based on a large spectrum of fluorophores, with excellent sensitivity, resolution, and speed. Spatiotemporal context is computationally reconstructed a posteriori.
smFISH/MERFISH
smFISH: State-of-the-art tool for the precise quantification at a very high spatial resolution of a small (1-10) to large (10-10000) number of transcripts. Compatible with the study of whole-mount samples.
Data analysis
Data analysis: Cutting-edge computational infrastructure and software innovations for image analysis (segmentation, deconvolution, and RNA spot detection) and bioinformatics (spatial reconstruction, lineage tracing).

Acknowledgements to Spatial-Cell-ID

To acknowledge Spatial-Cell-ID in your publications, please add the following sentence:

This work was supported by the EquipEx+ Spatial-Cell-ID under the "Investissements d'avenir" program (ANR-21-ESRE-00016).

Next Spatial-Cell-ID seminars

Read more
13
Sep
2026
Seminar
SCID 2026 Summer School
 
30
Apr
2026
Meeting
Equipex - 2026 Spatial-Cell-ID Day
 
02
Apr
2025
Meeting
Equipex+ Spatial-Cell-ID day
 

News

 Read more

Monday 14 September, 2026

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Transcriptomique spatiale : analyse de données et intégration scRNA-seq en Python
SpatialCellID logo
FORMATION CNRS - Transcriptomique spatiale par imagerie : du smFISH au FISH multiplexé

Thursday 20 March, 2025

Kick-off vignette
Job Offer: Engineer in Biological Techniques

Contact


SPATIAL-CELL-ID

ENS de Lyon
15 parvis René Descartes
BP 7000
69342 Lyon Cedex 07
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