The I3H Pipeline

Every Step Documented, Every Metric Tracked

Click any stage to expand its QC parameters, processing details, and quality benchmarks.

01
🩸
T + 0 min · Collection

Peripheral Blood Draw & PBMC Isolation

Whole blood collected via standard phlebotomy, PBMCs isolated through density gradient centrifugation within the processing window.

02
🔬
T + 4 hrs · Viability QC

Sample Viability & Cell Quality Assessment

Rigorous viability gating ensures only high-quality, representative samples enter the profiling pipeline.

03
🧪
T + 5 hrs · MDIPA Staining

Maxpar Direct Immune Profiling Assay (MDIPA)

Standardized lyophilized antibody cocktail – 30+ metal-conjugated markers measuring surface and intracellular proteins at single-cell resolution.

04
T + 8 hrs · CyTOF Acquisition

Mass Cytometry Data Acquisition

Cells are nebulized, ionized, and analyzed by time-of-flight mass spectrometry – 30+ parameters per cell at thousands of events per second.

05
🧹
T + 12 hrs · Data Processing

Bead Normalization, Gating & QC

Raw FCS files undergo bead normalization, debris removal, and standardized gating before entering the analysis pipeline.

06
🗄️
T + 24 hrs · Data Integration

Pennsieve Platform – Structured Data Management

Processed FCS files, annotations, and patient metadata organized in Pennsieve for discoverable, FAIR-compliant data management.

07
📊
T + 48 hrs · Analytics

Immune Fingerprinting & Informatics

Comprehensive immune fingerprints – quantifying 50 populations to establish baselines, detect perturbations, and track longitudinal trajectories.

Why This Matters

One Pipeline. One Panel. Thousands of Comparable Profiles.

4,000+Visits profiled with identical protocol
50Immune populations per fingerprint
< 48hBlood draw to analyzed fingerprint
0%Spectral overlap (mass cytometry)
≥ 85%Viability threshold for pipeline entry
FAIRData managed on Pennsieve platform