From Tissue
to Insight
Integrated Translational Pathology & Biomarker Solutions
Multiplex tissue imaging
Step 1
Scientific
Consultation
We align biology, endpoints, tissue requirements, platform strategy, and project outputs before launch.
Define the study question
Biology, endpoints, cohort and biomarker hypothesis
Platform selection
Based on tissue, biology and throughput
Sample feasibility
Tissue quality, ROI, specimen access and cohort planning
Project brief
Recommendation, QC gates, timeline and budget
PATHORABIOstrategy hub Pharma PI Biotech CSO Clinical PI Pathologist Study DefinitionBiology · endpoint · cohortBiomarker hypothesis and success criteriaSponsor and clinical context are aligned first. Platform SelectionMatched to tissue, biology and throughputPathora Bio recommends the platform strategyLinks Pharma PI, Clinical PI and Biotech CSO inputs. Sample FeasibilitySpecimen access · ROI · qualityClinical PI and pathologist confirm feasibility Project Brief✓ Platform recommendation✓ Sample and QC needs✓ Timeline and budget◌ Kickoff criteria
Step 2
Assay &
Platform Strategy
We move from pathology review to tissue QC, assay selection, panel verification, platform choice, and analysis strategy.
Expert Pathology Review
ROI, scoring logic and tissue context
Tissue & Assay QC
H&E, RNA quality, fixation and control tissue
Targeted Assays
IHC, ISH and RNAscope workflows
Panel Verification
Antibody bridging and reference controls
Spatial Platform Choice
Selected by biology, tissue and throughput
FISH / STED-FISH
Cytogenetic target localization
AI & Custom Analysis
Visiopharm, HALO, AtoMx, Python/R
PATHORA STRATEGY 1 · EXPERT PATHOLOGY ROI · tissue context · scoring 2 · TISSUE / ASSAY QC H&E · DV200 · RQN fixation · controls · autofluor. signal/background readiness 3 · TARGETED ASSAYS IHC · ISH · RNAscope ACD · Bond-III · Bond RX 4 · PANEL VERIFICATION antibody bridging · controls specificity · titration · S/B spectral balance · reproducibility 5 · SPATIAL PLATFORM biology · tissue · throughput ROI size · data requirements 6 · FISH / STED-FISH DNA/RNA localization cytogenetic readout 7 · AI / CUSTOM ANALYSIS Visiopharm · HALO · AtoMx Python · R HOVER A LEFT ITEM
Each step highlights its matching platform element.
Step 3
Sample Processing
& QC
Tissue processing with matched RNA, protein, staining, and panel-level QC before analysis.
Accessioning
Barcode tracking and chain of custody
RNA Quality QC
DV200 / RQN and pre-screening
Protein Assay QC
Fixation, antigen signal and controls
Sectioning
FFPE or cryo sections prepared for assay
Automated Staining
Bond-III / Bond RX workflows
Final QC Gates
Controls, bridging, panel and spectral QC
1 · ACCESSION Barcode / LIMS Chain of custody 2 · RNA QC DV200 / RQN RNA readiness gate 3 · PROTEIN QC fixation · antigen · controls S/B and specificity 4 · SECTIONING BLOCK 4–5 µm FFPE / cryo 5 · AUTO STAINING Bond-III / Bond RX IHC · ISH · IF · FISH 6 · FINAL ASSAY QC GATES Control Tissue reference sections Protein Signal specificity / background Antibody Bridging singleplex → multiplex Spectral QC unmixing / balance Batch QC run consistency RNA, protein, fluorescence, chromogenic, and barcode-based readout checks HOVER A LEFT ITEM
Each processing step highlights the matching RNA, protein, or assay QC checkpoint.
Step 4
Data Analysis
& Interpretation
Digital pathology, spatial analysis, and expert review convert images into biomarker-ready outputs.
Whole Slide Imaging
WSI review and ROI confirmation
Cell Segmentation
Visiopharm, HALO, QuPath, inForm
Biomarker Scoring
OD, H-score, Allred and positivity
Spatial Analysis
Loupe, Xenium, Space Ranger, AtoMx
AI & Custom Pipelines
Commercial tools plus Python/R
Interpretation & Sign-Off
Expert review before delivery
WHOLE SLIDE VIEWER — SEGMENTATION ROI review · cell detection · tissue segmentation BIOMARKER SCORING CD8+ TILs 74% PD-L1 H-score 240 Ki-67 positivity 43% Pathologist Sign-Off expert reviewed before delivery SPATIAL INTERACTION MAP SPATIAL TOOLS Loupe Browser Xenium Explorer Space Ranger AtoMx · GeoMx DSP cell neighborhoods · TME profiling · interaction mapping AI & CUSTOM ANALYSIS PIPELINE processing quantitative biomarker outputs 1 — Cell detection and QC 2 — Phenotype classification 3 — Spatial interaction mapping 4 — Statistical summaries 5 — Report-ready interpretation Visiopharm · HALO · QuPath · Python · R HOVER A LEFT ITEM
Hover a left item to highlight the matching analysis element.
Step 5
Secure
Data Delivery
Final deliverables are organized, reviewed, transferred securely, and packaged with traceable documentation.
Secure Client Portal
Encrypted upload and role-based access
Interactive Dashboard
Biomarker summaries and drill-down views
WSI Viewer
Annotated slides and shareable links
Deliverable Package
Report, WSI, data tables and raw archive
Audit Trail
QC records, metadata and version history
Scientific Report
Interpretation and pathologist sign-off
PATHORA BIO — SECURE CLIENT PORTAL 🔒 ENCRYPTED SAMPLES ANALYZED 248 BIOMARKERS 16× TURNAROUND 7d QC PASS RATE 98.7% BIOMARKER EXPRESSION OVERVIEW CD8 PD-L1 PD-1 FOXP3 Ki67 CD20 CD68 GZMB LAG3 DELIVERABLE PACKAGE 📄 Scientific_Report.pdf 🔬 WSI_Viewer_Link / SVS 📊 Quantified_Data.xlsx 🧬 Raw_Data_Archive.zip ✓ QC records ✓ Metadata ✓ Version history ✓ Access logs CAP / CLIA / GCP-aligned documentation · 24/7 access · encrypted · role-based access control SCIENTIFIC REVIEW & SIGN-OFF Interpretation reviewed before release to client HOVER A LEFT ITEM
Hover a left item to highlight the matching delivery element.
Accelerating translational discovery through integrated biomarker workflows
designed for biotech, pharma, and the patients who depend on them.
15+
Years Experience
5
Integrated Steps
CAP/CLIA
Aligned
End-to-End
Tissue to Insight
★
Intro
1
Consultation
2
Assay &
Platform
3
Processing
& QC
4
Analysis
5
Delivery
★
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Interactive Workflow

From Tissue to Insight

This interactive workflow is designed as a widescreen desktop presentation. For the best experience, view it on desktop or tablet. You can still continue on mobile if needed.

1 · Scientific Consultation
2 · Assay & Platform Strategy
3 · Sample Processing & QC
4 · Data Analysis & Interpretation
5 · Secure Data Delivery
Return to Innovation Contact Pathora Bio