QUANTITATIVE  Image Analysis

Multiplex Immunofluorescence Image Analysis​

Advanced Image Analysis:
Qualitative images to
quantifiable data​

As a spatial biology specialist, Propath’s bioinformatics service enables collaboration at any stage of the data journey. ​

Whether you’re working with your own data or have generated
these with one of our other services, we’re equipped to deal with
your research needs. From image hosting through to advanced
analysis and statistical support, our expert team can accelerate
discovery through every pixel.​

Introducing our service​​

  • Image hosting​
    Cloud-hosted image management with Pathcore, featuring advanced annotation tools and seamless team access and collaboration within a web browser
  • Fully Integrated Service
    A single end-to-end solution for sample processing, staining. imaging, hosting, analysis, and reporting
  • Platform Agnostic​
    Our services can analyse images regardless of the originating platform. If you have images, we can ensure seamless integration and comprehensive analysis
  • GCP Image Analysis
    We offer GCP-validated whole slide analysis using Visiopharm, leveraging deep learning and artificial intelligence for exploratory
    endpoints
  • 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

Image Analysis Service Menu​

  • Basic, advanced or bespoke packages​
    Different tier structure to suit your needs​​
  • 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​


CD68
FoxP3
CD8
PD1
PD-L1
Ki67
CK
CD4
CD20
CD3
Cytosolic
Nuclear
Membrane
Membrane
Membrane
Nuclear
Membrane
Membrane
Membrane
Membrane
Myeloid
Lymphoid
Lymphoid
Lymphoid, Myeloid
Lymphoid, Myeloid
Cancer, Epithelial
All proliferating cells
Epithelial
Lymphoid, Myeloid
Lymphoid
Lymphoid
Myeloid
Lymphoid
Lymphoid
Lymphoid, Myeloid
Lymphoid, Myeloid
Cancer, Epithelial
All proliferating cells
Epithelial
Lymphoid, Myeloid
Lymphoid
Lymphoid
Standard Advanced Bespoke
Routine tissue segmentation into 2 categories Bespoke tissue segmentation into up to 3 categories The Propath specialist Bioinformatics team are able to work with any image source including multi-omic integrated analyses. Fully customisable image processing pipelines include image normalisation, artefact or noise compensation and other deep learning models. Fully bespoke R scripting is available for downstream analysis, including integration of non-imaging data such as sequencing, flow cytometry and soluble biomarkers, as well as statistical support (link to Bioinformatics page)
Cell segmentation Addition of extra training to cell segmentation, if required
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 file Data provided as excel file and high-resolution figures

GCP validated workflow​

RNAscope in situ hybridization is being used by researchers to complement IHC and as an effective alternative to IHC

Step 1

Identify cells and tissue features​

Step 2

Extract features from labels and assign classes​

Step 3

Present data and interrogate spatial interaction​

Propath's tools for Image Sharing & Hosting​​

‌IHC is a complex, multi-parameter staining technique applied across variable fresh frozen and fixed paraffin embedded tissues.  As a result, developing an optimum staining protocol is not always straightforward.

Our experience informs our view that high quality IHC with strong signal intensity and low background staining can only be achieved by paying careful attention to the following factors:

New text to go here

01
High-resolution image display: view natively rendered whole slide images in the browser​
02
Zoom and navigation controls: full zoom, pan and rotate controls for a natural viewing experience ​
03
Full display controls: select channel combinations, set colours and adjust histograms to highlight the biology​
04
Annotation tools: Integrated tools enabling identification and markup of features and regions of interest​
05
Integrated analysis workflow: Bidirectional interface with Visiopharm to ensure a seamless training and
review of feature detection algorithms​
06
Cloud-hosted: easily share and distribute images and annotations with your team with a web link, or lock your
images with account-restricted access. ​

GCP Validated for Clinical Trials

The Propath 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 using:

  • Quality Management System
    Propath’s GxP Quality Management system ensures all systems, staff and processes are fit for the intended use and reviewed regularly
  • Development, Validation and Production
    Processes for development, validation and production execution of data pipelines are process 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 are validated and managed from image handling through image analysis, data analysis and sharing/transfer
  • Trained Staff
    All outputs are generated and/or reviewed by expert analysts trained to use the systems, processes and SOPs and in the principles of GCP

GCP Validated for Clinical Trials

  • Quality Management System
    Propath’s GxP Quality Management system ensures all systems, staff and processes are fit for the intended use and reviewed regularly
  • Development, Validation and Production
    Processes for development, validation and production execution of data pipelines are process 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 are validated and managed from image handling through image analysis, data analysis and sharing/transfer
  • Trained Staff
    All outputs are generated and/or reviewed by expert analysts trained to use the systems, processes and SOPs and in the principles of GCP

How our service works​

Whether you’re entering our pathway with imported images or generating images with Propath, we seamlessly convert qualitative images into quantitative data for statistical analysis and visualisation. In collaboration with pathologists or subject matter experts, algorithms are trained to extract and quantify features, providing robust and reproducible results.​

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.

‌Lunaphore COMET
Highly multiplexed sequential immunofluorescence for up to 40 protein on a single slide
‌Validated for GCP studies
‌Akoya PhenoCycler and PhenoImager
‌Ultra-high plex single-cell spatial phenotyping; and focused mIF panels for high-throughput translational research
‌Validated for GCP studies
‌RNAScope and BaseScope
Robust in situ hybridization technology for rapid quantification of any RNA target in any tissue with spatial context
‌Validated for GCP studies
Navinci Proximity Ligation
Assays
Automated PLA assays for the
detection of protein-protein
interactions and post-
translational modifications​
‌Validated for GCP studies

Examples of our 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

A selection of our work

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