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Transcriptomic and multiomic data analysis

Spatial Bioinformatics

From Discovery to Clinical Trial:
Bioinformatics for Biopharma

Extract biological insights from spatially‑resolved multiomic data.

Propath Spatial Data Analysis Service empowers researchers and clinical teams to decode biological processes through integration of high‑resolution multiomic datasets.

Leveraging in-house workflows in a GCP‑validated environment, we provide robust, reproducible and regulatory‑ready analyses suitable for both exploratory research and clinical trial environments.

Spatially resolved transcriptomics imagery
Spatial phenotype map of atherosclerotic plaque
Lab technician reviewing cell
Differential gene expression analysis

Introducing our service​​

  • Scientist-led, specialist spatial team
    Propath’s biologist-driven solution for interpreting the complex, spatially resolved datasets generated by spatial transcriptomics and spatial proteomics experiments
  • A fully integrated service
    A single, validated, end-to-end solution for sample processing, staining, imaging, hosting, analysis and reporting
  • Platform agnostic​
    Our service can analyse data regardless of the originating platform. If you have spatially resolved data, we can provide insightful and comprehensive analysis
  • GCP validated R scripting for clinical trial analyses
    Clinical trial compliant analyses available from a range of pre-developed solutions and fully custom scripting, all within Propath’s GCP-ready data platform
  • Standalone service
    Tailored, specific services to complement existing workflows, offering flexibility and cost-effectiveness
  • Multiomics
    Our services allow integration of multiple data sources, both spatial and non-spatial: IHC, H&E/Histology, mIF, IMC, 10x, GeoMx and CosMx

How our service works​

Propath’s team of experienced data scientists work interactively to advise laboratory experimental design and to build routine data pipelines or bespoke solutions, providing robust and reproducible analyses and presenting them accessibly for the relevant stakeholders in support of each step of your pathway, from discovery to clinical trials.

Data

Sorted

Arranged

Presented

Explained

Data

Sorted

Arranged

Presented

Explained

Multiomic analysis service menu​

Propath's interactive report

  • Basic, advanced or bespoke packages​
    Different tier structures to suit sponsor requirements​​
  • QC and normalisation
    Including batch correction
  • Dimension reduction
    Simplifying data
  • Modelling and statistics
    Clustering, comparisons and significance
  • Interactive report
    Data compilation, presentation and sharing
  • Multiomic integration
    Integration of modalities and analytes

Data analysis examples

Propath offers a range of predeveloped analysis packages and standardised outputs tailored to the analyte and data type. Packages may also be customised, multiple methodologies integrated or fully bespoke scripting developed on request.

Common outputs
  • Cell and tissue segmentation maps
  • Pathway Analysis
  • Spatial Interactions / Neighbourhood
  • Cellular responses

SlideSeq (GeoMx/Visium/Stereo-seq/Illumina)

  • Differential Gene Expression
  • Pathway Analysis
  • Spatial Overlays
  • Pseudotime
  • Single Cell Deconvolution
  • Hotspot Analysis
  • Variant Calling

In-situ transcriptomics (CosMx/Xenium/Vizgen)

  • Differential Gene Expression
  • Pathway Analysis
  • Spatial Overlays
  • Pseudotime
  • Cell Typing
  • Neighbourhood Analysis
  • Cell-cell interactions
  • Resegmentation

Multiplex Fluorescence

  • Cell and tissue segmentations
  • Pathway Transduction
  • Spatial interactions
  • Cellular responses

In-situ transcriptomics (CosMx/Xenium/Vizgen)

  • Differential target expression
  • Pathway Analysis
  • Spatial Overlays
  • Pseudotime
  • Cell typing
  • Neighbourhood Analysis
  • Cell-cell interactions
  • Extracellular analysis

Integrate with bulk datasets

nCounter
  • DGE with custom modelling
  • Pathway analysis
  • Cell Deconvolution
scRNAseq
  • Cell Typing
  • Annotation of spatial transcriptomics
  • Cell typing reference library
Flow Cytometry
  • Cell typing
  • Phenotype Discovery
  • mIF analysis design

How our service works​

Propath’s team of experienced data scientists work interactively to advise laboratory experimental design and to build routine data pipelines or bespoke solutions, providing robust and reproducible analyses and presenting them accessibly for the relevant stakeholders in support of each step of your pathway, from discovery to clinical trials.

GCP validated for clinical trials

Propath's platform for quantitative image analysis and bioinformatics has been designed and validated to be fit-for-purpose for use on clinical trial data.

Our controlled environment ensures analyses are conducted according to the principles of informed consent, data integrity, confidentiality and scientific rigour to maintain GCP compliance from sample receipt to data delivery.

  • Quality Management System
    Propath’s GxP Quality Management System ensures all systems, staff and processes are fit for purpose and reviewed regularly
  • Development, validation and production
    Processes for development, validation and production execution of data pipelines are all controlled by SOPs
  • Risk and review
    ‌Risk-based approach to management of systems, processes and methods (including the use of AI models) ensures fit-for-purpose controls and reviews
  • Validated systems
    All software in the pipeline is validated and managed from image handling through image analysis, data analysis and sharing/transfer
  • Trained staff
    Outputs are generated and/or reviewed by experienced analysts trained to use the systems, processes and SOPs and in the principles of GCP

Challenges interpreting spatial data

Platform heterogeneity

No standardised format, resolution or content depth
Omic-silo

Transcriptomics, proteomics, and metabolomics data integration
Analytical units

Need to segment data into spatial unit (cells, tissues etc)
Tissue quality

Varying tissue quality impacts data quality and consistency

‌Propath’s solution for spatial biology

Platform agnostic

In-house tools developed independent for compatibility
Spatial Aware QC

Quality check and normalisation tools specific to tissue complexity
GCP validated

Pre-validated platform is audit ready
Scientist led

Experienced spatial biologists support robust analysis design and execution

A selection of Propath's work

Spatial plot showing cell phenotype locations generated from single cell spatial transcriptomic analysis of atherosclerotic plaque
UMAP plots clustered by gene expression and coloured by cell type annotation (Census vasculature signature), split by lesion severity
Cleveland dot chart showing distribution of viral RNA across cell phenotypes, globally (coloured) and per field (grey)
CosMx image showing cell segmentation in teal, viral RNA in red and yellow (right), Spatial phenotype map displaying viral positive cells with a red circle (left)
Spatial gene expression of CA-IX mRNA across an HNSCC section from a GeoMx experiment, showing CA-IX protein by immunofluorescence in red
Cell proportion estimated per ROI using cell deconvolution by SpatialDecon, annotated according to sample group and CA-IX expression by IHC

FAQs

Advanced platforms for spatial biology available today at Propath

‌Our experience across a range of platforms for spatial biology allows us to recommend the most appropriate platform for each research project.

We understand the strengths and limitations of each platform – and how to get the best out of them.

RNAScope and BaseScope
Robust in situ hybridization technology for rapid quantification of any RNA target in any tissue with spatial context
PhenoCycler and PhenoImager
High plex single-cell spatial phenotyping; and focused mIF panels for high-throughput translational research
COMET
Highly multiplexed sequential immunofluorescence for up to 40 protein on a single slide
nCounter, GeoMx and Cosmx
Integrated spatial multi-omics including up to whole transcriptome profiling from tissue to sub-cellular resolution
nCounter, GeoMx and Cosmx
Integrated spatial multi-omics including up to whole transcriptome profiling from tissue to sub-cellular resolution
RNAscope and COMET
High-plex and focussed multi-omic mIF panels supporting discovery and translational studies
Xenium
Targeted, scalable spatial transcriptomics and multi-omics panels at subcellular resolution
PhenoCycler and PhenoImager
High-plex and focussed mIF panels supporting discovery and translational studies
Proximity Ligation Assays
Automated PLA assays for the detection of protein-protein interactions and post- translational modifications​

Outsourced R&D - Done better.

At Propath we approach biopharma R&D differently. Say goodbye to Large CRO frustrations –and hello to a more responsive, agile and efficient level of service.