Resources
Protocols • Tools • Documentation
Everything you need to design, run, and analyze a cytometry experiment — from panel design tools and spectra viewers to sample preparation protocols, analysis software, and cell marker databases. Click on each section below to expand.
- A. Panel Design & Fluorochrome Selection Tools
Choose fluorochromes before committing reagents. These free tools model spectral overlap and laser/detector configurations for instruments at this core.
FluoroFinder Panel Builder
Recommended: All Instruments
Build multi-color panels with real-time spillover calculations. Supports 40+ instrument configurations including Cytek Aurora 5L and BD FACSAria. Visualizes spectral overlap matrix and suggests low-spillover fluorochrome alternatives. Free with registration.
Best for: all instruments — Aurora, FACSAria II
Cytek® Assay Builder
Recommended: Aurora Panels
Purpose-built for the Cytek Aurora. Models spectral unmixing across all 64 detectors of the 5-laser configuration. Predicts unmixing error for each fluorochrome pair and highlights problematic combinations. Essential before designing any Aurora panel.
Best for: Cytek Aurora 5L spectral panels
https://cloud.cytekbio.com/dashboard
BioLegend Panel Designer
Panel builder
Build panels using BioLegend's catalog with automated compatibility checking. Generates a printable panel summary with clone, catalog number, and recommended dilution. Integrates directly with the BioLegend Spectra Analyzer.
https://www.biolegend.com/en-us/panel-builder
BD Horizon™ Panel Designer
Panel builder
Designs panels using BD Horizon BV and BUV dye series. Includes a spillover matrix calculator and instrument-specific detector configuration.
Best for: BD FACSAria II panels
https://www.bdbiosciences.com/en-us/resources/panel-design?tab=Overview
Thermo Fisher Flow Panel Builder
Panel builder
Builds panels using Invitrogen antibodies. Generates protocol-ready panel tables with validated clone/fluorochrome combinations for common immune cell subsets.
https://www.thermofisher.com/order/panel-builder/#!/
Miltenyi REAfinity™ Panel Builder
Panel builder: CyTOF compatible
Ideal for recombinant antibodies (REAfinity clones) with minimal lot-to-lot variation. Includes pre-designed panels for human and mouse immunology. Companion tool available for Maxpar CyTOF panel design.
https://www.miltenyibiotec.com/US-en/resources/tools/flow-cytometry-panel-builder.html
- B. Fluorescence Spectra Viewers
Visualize excitation and emission spectra before finalizing your panel. Critical for understanding spectral overlap in both conventional and spectral cytometry.
BioLegend Spectra Analyzer
Spectra viewer
Overlay multiple fluorochrome spectra against any laser/detector configuration. Covers 400+ fluorochromes and tandem dyes with real measured spectra. One of the most comprehensive databases — exportable as PDF.
https://www.biolegend.com/en-us/spectra-analyzer
BD Spectrum Viewer
Spectra viewer
Shows emission and excitation curves for BD reagents with predicted spillover values between detector channels. Especially useful for optimizing BV (Brilliant Violet) and BUV (Brilliant Ultraviolet) combinations.
https://www.bdbiosciences.com/en-us/resources/bd-spectrum-viewer
Thermo Fisher Spectra Viewer
Spectra viewer
Covers Alexa Fluor, eFluor, LIVE/DEAD, and other Thermo reagents. Plots predicted percent transmission through user-defined bandpass filters.
- C. Data Analysis Software
FlowJo v10
Commercial: Available on-site (NA2.308)
Gold standard for flow cytometry analysis. Features hierarchical gating, compensation editing, statistics, and plugins for UMAP, tSNE, and FlowSOM dimensionality reduction.
Free training: https://www.flowjo.com/
OMIQ
Cloud-basied: Core account available
Cloud platform for high-dimensional analysis — no coding required. Drag-and-drop UMAP, FlowSOM, PhenoGraph, and gating. Ideal for spectral and CyTOF data. Ask core staff for access.
CytoBank
Cloud-basied: Free academic account
Cloud platform with viSNE (tSNE), CITRUS, and SPADE algorithms. Widely used in translational and clinical immunology studies.
CATALYST (R/Bioconductor)
Open source: R
CyTOF preprocessing, normalization, batch correction, dimensionality reduction, and differential abundance/state analysis. Pairs with diffcyt for statistical testing.
https://bioconductor.org/packages/release/bioc/html/CATALYST.html
Scanpy / AnnData (Python)
Open source: Python
Python framework for single-cell analysis. Supports Leiden/Louvain clustering, UMAP, trajectory analysis, and differential testing. FCS files imported via readfcs or anndata.
https://scanpy.readthedocs.io/
IDEAS® (Amnis ImageStream)
Commercial: Available on-site
Dedicated software for ImageStream imaging flow cytometry. Combines quantitative image feature analysis (morphology, co-localization, texture) with standard flow gating.
- D. Cell Marker & Antibody Databases
Find validated markers, clones, and antibodies for cell populations of interest.
CellMarker 2.0
Database
Curated database of cell-type markers from published literature. Covers 4,000+ cell types across human and mouse. Search by tissue, disease, or cell type and export marker lists for panel design.
http://biocc.hrbmu.edu.cn/CellMarker/
Human Protein Atlas — Immune Cells
Database
Protein expression data across 28 human immune cell types with flow cytometry validated data. Excellent for identifying unique surface markers and cross-reactivity risks.
https://www.proteinatlas.org/humanproteome/immune+cell
Antibodypedia
Database
Cross-vendor antibody search engine with validation filters for flow cytometry, IHC, and western blot. Shows clone history and user-submitted validation data.
https://www.antibodypedia.com/
ImmPort
NIH Data repository
NIH-funded immunology repository with curated flow cytometry FCS files and panel definitions from published studies. Useful for benchmarking panels against published immune monitoring data.
Human Cell Atlas
Reference atlas
Single-cell reference atlas of human tissues. Provides marker profiles for rare and tissue-resident cell types. Particularly useful for non-PBMC CyTOF panel design.
https://www.humancellatlas.org/
Maxpar® Human Immune Monitoring Panel (Standard BioTools)
CyTOF reference panel
30-marker CyTOF reference panel for comprehensive human immune phenotyping of all major PBMC populations. A validated starting point for mass cytometry panel design.
- E. Education, Training & Reporting Standards
FlowJo University
Free training
Self-paced courses on gating strategies, compensation, dimensionality reduction, and spectral unmixing. Certificate programs available. Highly recommended for all new core users before their first instrument session.
https://www.flowjo.com/learn/flowjo-university
ISAC — International Society for Advancement of Cytometry
Professional society
Primary professional society for cytometry. Publishes Cytometry A and Cytometry B, hosts the annual CYTO meeting, and provides the MIFlowCyt reporting standard required by many journals.
MIFlowCyt — Reporting Standard
Required by many journals
Minimum Information about a Flow Cytometry Experiment. Required by Cytometry A, JEM, and J Immunol. Covers instrument settings, reagent documentation, and gating strategy requirements. Review before manuscript submission.
https://isac-net.org/miflowcyt-2/
Cytek Biosciences Resource Library
Webinars and app notes
Webinars, application notes, and protocols for spectral flow cytometry on the Aurora. Covers unmixing theory, antibody titration, rare-event detection, and full-spectrum panel design.
https://cytekbio.com/pages/resources
Standard BioTools (Fluidigm) Resource Library
CyTOF resources
CyTOF protocols, metal conjugation guides, and data analysis tutorials for Helios and Hyperion instruments. Essential reading before designing a first mass cytometry experiment.
https://standardbio.com/resources/
BD Biosciences Knowledge Center
Technical guides
Guides on compensation, panel design, instrument optimization, cell sorting, intracellular staining, and rare-event analysis. Includes instrument-specific troubleshooting documents.
https://www.bdbiosciences.com/en-us/resources/knowledge-center