Transcriptomic and multiomic data analysis

Spatial Bioinformatics

From Discovery to Clinical Trial:
Bioinformatics for Biopharma

Extract Biological Insights From Spatially‑Resolved multiomic data sets.

Propath Spatial Data Analysis Services empower 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 (left) of atherosclerotic plaque generated from single-cell transcriptomics data (Right)

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
Multi-omics
Our services allow integration of multiple data sources, both spatial and non-spatial: IHC, H&E/Histology, mIF, IMC, spatial transcriptomics and bulk sequencing

Data

Sorted

Arranged

Presented

Explained

Image analysis service menu

T-cell to macrophage nearest neighbour analysis

Basic, advanced or bespoke packages
Different tier structures to suit sponsor requirements
Image QC
Quantitative and qualitative image QC metrics
Tissue segmentation
Understanding cellular relationships within separate tissue
categories
Cell segmentation and phenotyping
Defining cellular boundaries using nuclei dilation or bespoke
AI-algorithms
Advanced data analysis
Downstream data analysis to aid interpretation

A closer look at image analysis tiers

Get in touch

Standard	Advanced	Bespoke
Routine artefact detection	Bespoke artefact detection	Any image from any source with the option to integrate with other multi-omic data Fully customisable image processing pipelines include image normalisation, artefact or noise compensation and other deep learning models Fully bespoke R scripting available for downstream analysis, including integration of non-imaging data such as sequencing, flow cytometry and soluble biomarkers Statistical support including a range of bioinformatics options
Routine tissue segmentation into two categories	Bespoke tissue segmentation
Cell segmentation	Bespoke cell segmentation
Cell phenotyping	Cell phenotyping
Spatial Analysis - Density analysis, average counts within, nearest neighbour	Spatial Analysis - Density analysis, average counts within, nearest neighbour, distance to category edge, neighbourhood analysis
Data provided as excel and high-resolution figures	Data provided as excel and interactive plots

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

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.

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.

PhenoCycler and PhenoImager

High plex single-cell spatial phenotyping; and focused mIF panels for high-throughput translational research

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

Proximity Ligation Assays

Automated PLA assays for the detection of protein-protein interactions and post- translational modifications

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

RNAScope and BaseScope

Robust in situ hybridization technology for rapid quantification of any RNA target in any tissue with spatial context

nCounter, GeoMx and Cosmx

Integrated spatial multi-omics including up to whole transcriptome profiling from tissue to sub-cellular resolution

PhenoCycler and PhenoImager

High-plex and focussed mIF panels supporting discovery and translational studies

A selection of Propath's work

isPLA analysis highlighting receptor-ligand binding in pink, interacting cells in red and non-interacting cells in blue

AI guided spatial transcriptomics analysis investigating role of hypoxia in immune cell exclusion in head and neck cancer

Artefact detection demonstrating exclusion of erythrocytes while retaining lower signal from fluor labelled antibody

AAV distribution analysis including glomerulus detection, cell segmentation and classification with RNAscope quantification

Bespoke sensory neuron and satellite cell segmentation for in-situ gene expression assay by CosMx in dorsal root ganglion

Spatial plot representing immune cell phenotypes assigned from a mIF stain generated by COMET on atopic dermatitis

FAQs

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.

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