CYTO+ is a specialized computational service for spectral flow cytometry analysis that bridges the gap between high-dimensional data generation and biological interpretation. We provide standardized panel design, AI-assisted immunophenotyping, and automated workflows for researchers at CAU and UKSH.
- Automate analysis with AI-driven clustering tools and machine learning.
- Utilize a validated 43-parameter panel for comprehensive immune profiling.
- Reduce batch effects via standardized panel design and preprocessing protocols.
- Access expert support for study planning.
Why Choose CYTO+?
- Comprehensive workflow integration: From antibody selection to publication-ready dashboards, CYTO+ provides end-to-end support for spectral cytometry projects.
- Standardized protocols: Optimized SOPs for sample biobanking, staining, and clinical standardization ensure reproducible, high-quality data across batches.
- AI-powered analysis: Automated clustering, UMAP visualization, and LLM-assisted cell population annotation eliminate manual gating bottlenecks.
- Reduced batch effects: Unified panel design and automated preprocessing minimize technical variability in patient cohorts.
- Expert support: Led by Dr. Henry Nording with dedicated AI-cytometry technical support from Jacob von Esebeck.
The CYTO+ Panel: 37+6 Spectral OMIP
CYTO+ employs a validated 43-parameter spectral flow cytometry panel optimized for 5-laser systems (Cytek Aurora), balancing comprehensive immune coverage with experimental flexibility.
Panel architecture:
- 37-marker backbone: Covers all major leukocyte populations in human peripheral blood with resolution comparable to OMIP-069
- T cells: Naïve, central/effector memory (TCM/TEM), TEMRA, regulatory T cells (naïve/activated Tregs), MAIT cells, and Th1/Th2 subsets via chemokine receptor profiling.
- Myeloid cells: Monocytes (classical/intermediate/non-classical), dendritic cells (cDC1, cDC2, pDC), and basophils.
- Lymphocytes: B cells (naïve, marginal zone-like, memory, plasmablasts), NK cells (CD56dim/bright), innate lymphoid cells (ILCs).
- Rare populations: Circulating endothelial cells (CD45⁻CD31⁺).
- 6 flexible drop-in channels: Pre-allocated slots for disease- or context-specific markers (e.g., checkpoint inhibitors PD-1, TIGIT; activation markers CD69, CD152; tissue-specific antigens) without disrupting backbone resolution.
- Low complexity index: 26.66 (vs. 53.72 for OMIP-069), enabling robust spectral unmixing with minimal interference.
Sample compatibility:
Validated for cryopreserved PBMCs, RBC-lysed whole blood, and PROT1-stabilized samples.
Service Packages
CYTO+ offers modular service tiers to support projects from initial planning through publication.
Package
| Description
| Fee
|
Starter | Panel feasibility check and up to 3 hours of design coaching, including evaluation of fluorochrome-marker combinations and antibody titration strategies. | 90 € |
Study Planning | Guidance on sample collection, RBC lysis/fixation protocols, quality-control run, and pilot measurement (two half-day sessions). | 300 € |
Deep-Insight | Machine learning cluster analysis with interactive heatmaps and dashboards; includes user onboarding to the analysis pipeline (two half-day sessions). | 300 € |
Academy (scheduled when minimum enrollment is reached) | Intensive two-day hands-on coding workshop covering spectral unmixing, R-based analysis pipeline operation, and custom workflow adaptation. Scheduled when minimum enrollment is reached (typically 6–8 participants). Includes course materials, sample datasets, and certificate of completion. To express interest or inquire about the next scheduled session, please contact Jacob von Esebeck (Jacob.vonEsebeck@uksh.de). Participants should have basic familiarity with R programming; introductory materials will be provided upon registration. | TBA* |
How to Use CYTO+
Step 1: Initial consultation
Contact the CYTO+ team via email or phone to discuss your research question. CYTO+ provides flexible entry points depending on your project stage and analysis needs. Whether you have existing high-dimensional data requiring expert analysis, are planning a new spectral cytometry experiment, or wish to develop in-house analysis capabilities, CYTO+ offers tailored support pathways.
Find your starting point:
- Existing data analysis: You have spectral flow cytometry data and need AI-assisted clustering, annotation, and interpretation → Deep-Insight package.
- Experiment planning: You’re designing a new study and need panel design guidance or marker selection support → Starter consultation.
- Complete study support: You need end-to-end assistance from experimental design through data analysis for clinical or longitudinal studies → combine Study Planning + Deep-Insight.
- Learn to analyze independently: You want hands-on training in R-based workflows and the CYTO+ pipeline → Academy workshop (scheduled on demand).
- Custom support: Need individual pipeline assistance, troubleshooting, or specialized analysis? We offer personalized consultation beyond standard packages.
Step 2: Computational support
CYTO+ operates like a flow cytometry core facility—only the “instrument time” is compute time and expert guidance for high‑dimensional flow cytometry analysis. Depending on the dataset size and your preferred working style, analysis can run on CYTO+ workstations (remote access) or on the CAU HPC cluster for large datasets with high event counts.
- CYTO+ Analysis Workstations
- Operation mode: Autonomous usage (remote access) or assisted analysis sessions
- Specifications: High-performance workstations optimized for spectral flow cytometry data
- Capacity: Suitable for small to medium-sized datasets (up to ~20–30 million total events after cleaning)
- Booking: Reservable via the online booking system under “Cytometry Equipment”
- Features: Pre-installed CYTO+ R-pipeline environment, FlowJo, and SpectroFlo for post-acquisition analysis
- For larger datasets: CYTO+ supports execution on the CAU HPC cluster (including cluster-ready workflows).
- Support model (per hour)
- Full service: CYTO+ runs the pipeline for you and delivers curated results and dashboards.
- Assisted usage: CYTO+ works with you per hour while teaching you how to run the established workflows (best suited for users who can read and adapt R code, without writing everything from scratch).
- What the pipeline covers (end-to-end)
- Preprocessing & QC: per-file debris gating, fixed compensation handling, debris/doublet/dead-cell exclusion using a “molecular ruler”, robust logicle transformation, gaussNorm (or KDE-based) normalization, trimming, and batch-effect detection visualizations.
- Clustering & curation: FlowSOM clustering, clustering-depth assessment, UMAP, metadata overlays (e.g., hexbins), and systematic artifact detection/curation (dominated clusters, very small clusters, mixed-lineage clusters, mutually exclusive clusters driven by residual batch effects).
- Annotation & readouts: AI-assisted cluster naming and downstream feature/readout extraction designed for real-world patient datasets and trait correlations.
- UI-first exploration (optional)
- Shiny-based dashboards (e.g., ShinyCell2) enable interactive exploration of processed data without day-to-day coding, while keeping the full analysis reproducible and scriptable.
Step 3: Ongoing collaboration
CYTO+ supports iterative refinement of analyses, follow-up experiments, and multi-omics integration (e.g., linking flow cytometry phenotypes with transcriptomic or proteomic data via the university’s Bioinformatics Platform). Schedule additional consultations as needed to discuss findings, troubleshoot technical challenges, or plan publication strategies.
Getting Started
Contact the CYTO+ team to schedule an initial consultation (no charge) to discuss your project and identify the optimal service pathway:
- CYTO+ Responsible Scientist: Dr. med. Henry Nording (Henry.Nording@uksh.de)
- AI-Cytometry Technician: Jacob von Esebeck (Jacob.vonEsebeck@uksh.de)
- General enquiries: cytometry.corefacility@uksh.de
FAQs: Frequently Asked Questions
Do I need to use the standard 37+6 panel?
No. While the 37+6 backbone is validated for comprehensive immune monitoring, we fully support custom panel design. You can modify the six drop-in channels or collaborate with us to build a completely bespoke high-dimensional panel tailored to your specific research question.
Can I analyze my own external datasets with CYTO+?
Yes. We accept high-dimensional spectral flow cytometry data from any source (e.g., external core facilities or public repositories). Our Deep-Insight package is designed to process and normalize external datasets, provided they meet basic quality standards (which we assess during the initial consultation).
Is CYTO+ suitable for clinical multi-center studies?
Absolutely. Our pipeline is optimized for clinical cytometry cohorts. We provide standardized SOPs, batch-normalization strategies (gaussNorm), and robust quality control protocols specifically designed to minimize site-to-site variability and batch effects in longitudinal patient studies.
How is data security handled?
Patient-related analyses are performed within the firewall-protected UKSH clinical network to keep identifiable information inside the hospital IT environment. For compute-intensive runs on CAU high-performance resources and the German National High-Performance Computing network (NHR), only fully anonymized research datasets are used, in line with NHR data protection rules. NHR explicitly states that storing or processing research data containing personal information on NHR systems is prohibited and recommends working with anonymized data.
How does CYTO+ differ from the standard Cytometry Facility?
The standard CYTO facility focuses on instrument operation and cell sorting. CYTO+ operates as a computational core, focusing exclusively on what happens before (panel design, sample prep) and after acquisition (spectral unmixing, AI-driven clustering, biological interpretation).