Spatial Biology Core (SBC)

Home » Our Research » Core Facilities » Spatial Biology Core (SBC)

MMA-2_use-this-instead-min-min-min-2-768x512

The Spatial Biology Core (SBC) at the Cancer Science Institute of Singapore (CSI) offers a range of capabilities for cellular and tissue imaging that supports both translational and fundamental biology research. Our capabilities span two broad areas: spatial biology and bioimaging.

Spatial biology:

Our spatial biology capabilities can facilitate biomarker discovery and/or validation from formalin-fixed paraffin-embedded (FFPE) or fresh/frozen human tissue. Biomarkers can range from a single protein or RNA transcript to complex transcriptomic signatures, novel cell subtypes, or unique cellular spatial patterns.

These platforms also enable a deep interrogation of the immune microenvironment in both human and mouse tissue, priming the discovery of new biology such as novel spatial arrangements between stromal and epithelial/tumour cells, or transcriptomic differences between cells residing in distinct cellular compartments.

We provide fee-for-service options for the following capabilities:

1) Staining of protein-based markers in FFPE cells/tissue:

DAB immunohistochemistry (IHC) staining
Akoya Opal-TSA staining (multiplexed IHC)

2) Quantitative imaging for low-plex and high-plex multiplex IHC:

Akoya PhenoImager (low-plex)
Akoya PhenoCycler (high-plex)

3) Spatial transcriptomics and proteomics:

NanoString GeoMx
NanoString nCounter

4) AI-based analysis of high-content data:

Akoya inForm
Visiopharm

5) Training and consultation services to assist researchers with experimental design and development of bespoke protocols.

Bioimaging:

We have a range of microscopy platforms that facilitate the pursuit of fundamental biological questions pertaining to protein expression, localisation, and protein-protein interactions. We also have systems available for live cell imaging- both phase-contrast and fluorescence- and for high-content screening to evaluate morphological or viability changes in response to drug treatment or other modifying conditions.

The following systems are available in user-operated mode or, if assistance is required, staff-operated mode:

Widefield/epifluorescence imaging
- Zeiss Axio Imager M2
Confocal imaging
- Zeiss LSM 880
- Leica SP8
- Nikon A1R
Live-cell imaging
- Echo Cellcyte
- Zeiss Axio Observer Z1
High-content screening
- Revvity Opera Phenix Plus

For further information, please email “Spatial Biology Core” csi_spatial@nus.edu.sg

Resources

𝐅𝐢𝐠𝐮𝐫𝐞 𝟏: Capabilities and resources at Spatial Biology Core

𝐅𝐢𝐠𝐮𝐫𝐞 𝟐: At SBC we consider ourselves a “one-stop shop” for spatial biology. The above figure describes an optional workflow by which to utilise our services: 1) high-plex single-cell resolved IHC ( PhenoCycler) will facilitate the discovery and quantification of novel cell populations and/or uncover unique spatial patterns; 2) the biology of these novel cell populations can be further interrogated by the GeoMx Digital Spatial Profiler platform, where the transcriptome of specific cell types can be compared and contrasted between distinct tissue compartments (e.g. tumour vs stroma); finally (3) putative biomarkers identified (cell types or spatial patterns) can be validated in patient samples (retrospectively or prospectively) using low-plex multiplexed IHC (Opal-TSA staining) and scanning on the high-throughput PhenoImager HT ( which can scan up to 80 slides in a single run). [Figure created by BioRender]