Spatial
SCOP offers imaging-based spatial services, which enables in situ analysis at subcellular resolution on fresh frozen (FF) and formalin fixed paraffin embedded (FFPE) tissue with the Xenium Analyzer (10x Genomics).
Services
Spatial RNA
Spatial RNA, imaging-based spatial transcriptomics on the Xenium Analyzer. Choose either predefined gene panels or customize your own panels based on your genes of interest.
Spatial RNA & Protein
Spatial RNA & Protein, imaging-based spatial transcriptomics on the Xenium Analyzer with subcellular resolution of both transcripts and protein expression. Choose both RNA (predefined or custom) and predefined protein panels.
Guidelines
Please read through our guidelines below.
Good quality tissue is essential for good data!
- Tissue sectioning: Test your tissue sectioning on regular glass slides before mounting tissue sections on Xenium slides.
- QC: Assess tissue morphology by performing DAPI and H&E tissue staining. For more details, please go visit 10x Genomics website.
- Probe panels: Choose a panel that is suited for the research project: 10x Genomics pre-designed panels, custom add-ons, standalone custom, advanced custom panels (e.g. other species). If add-on or custom probe panels are required, design and order probes through 10x Genomics (due to IP rights). Remember to send the probe j.son file to SCOP.
Need help with tissue sectioning? Contact RMPP for assistance.
Xenium slides with tissue mounted are delivered to SCOP
- Tissue detachment test (optionable)
- Slide preparation and Xenium Analyzer*
- Xenium Ranger output files
- Re-segmented with a custom Cellpose model (if applicable).
*SCOP does not support tissue sectioning. Please contact RMPP for assistance.
If requested, SCOP offers additional computation services for spatial transcriptomics, including:
- Secondary segmentation with Cellpose, for cases where primary segmentation requires optimization. Please note that SCOP does not develop or train models however, we provide guidance and computational support for data re-segmentation.
- Segmentation refinement using Baysor
- Data integration using scvi-tools.
- Combined clustering and cell type annotation across slides using label transfer with a user-provided reference. Please note that this is dependent on the quality and resolution of the reference dataset.
- Creation of annotated data objects with combined clustering and cell type labels, in a format compatible with Xenium Explorer.
The price for a spatial project depends on various factors, including the number of slides, selected probe panels (RNA/protein), and optional cell segmentation staining. Contact SCOP to receive a quote.
Please recognize and acknowledge SCOP’s contributions to the scientific improvements in your project. Being acknowledged in publications is very important as it serves as documentation for the SCOPS's value and performance.