A flow cytometry template that adapts to your lab's panels.
This flow cytometry template ships with a 10-step protocol, validated antibody panel references, pre-wired compensation and gating fields, and structured inputs for sample source, fluorochrome panel, voltage settings, total events collected, and gated population percentages. Your lab edits the configuration to match the panel and sample type you actually run, instead of rebuilding the panel record from scratch every experiment.
See exactly how the template loads in ELabELN.
This is the live ELabELN experiment view, the same screen your lab works in every day. Switch between a blank start and a fully populated example, then expand any section to see what the template pre-fills.
What this flow cytometry template ships with.
This flow cytometry template ships configured for a five-color T cell phenotyping panel on peripheral blood mononuclear cells (PBMCs), with a 10-step protocol covering PBMC isolation through compensated gating and population frequency export. The protocol assumes a BD FACSAria III or similar cytometer with a 488 nm and 405 nm laser, a CD3-BV421 / CD4-FITC / CD8-PE / CD45-PerCP / Live-Dead-APC five-color panel, single-color compensation controls, FMO controls for marker boundaries, and 100,000 collected events per sample.
Structured fields capture sample, panel, and acquisition metadata in typed inputs (sample source, isolation method, viability before stain, fluorochrome panel composition, antibody titers, compensation status, total events, gated percentages for major populations), so panel composition and acquisition parameters are queryable across runs instead of buried in free text. Antibody aliquots, the viability dye, and titrated working dilutions link to the ELabELN inventory so panel reproducibility flows into the experiment record without manual entry. The spreadsheet editor captures gated population frequencies (CD3+, CD3+CD4+, CD3+CD8+, CD4:CD8 ratio) with the ability to attach raw FCS export references.
The template is intended as a tested baseline for academic and life sciences research labs running immunophenotyping, intracellular cytokine staining, cell-cycle analysis, apoptosis assays, or any flow-based cell analysis. Configure the panel, swap the sample source, adjust acquisition parameters, or change the gating strategy to match the analysis your lab actually runs. ELabELN's tamper-evident audit trail captures every panel composition, every compensation run, and every gated frequency, so the resulting record supports panel-version documentation, multi-PI collaboration on shared cohorts, and FDA 21 CFR Part 11 review when the lab's quality system requires it.
Every ELN section, pre-populated for flow cytometry.
The template populates the existing ELabELN sections your lab already works with: Main Text, Extra Fields, Steps, Compounds, Links, and more. Your team edits instead of building from scratch.
Main Text
Panel design notes, sample source notes, and expected population frequency ranges, written in the TinyMCE editor.
- Objective + panel scaffold
- Compensation strategy notes
- Linked to upstream PBMC isolation
Extra Fields
Twelve structured, typed fields grouped by Sample, Panel, and Acquisition & Gating.
- Sample source, viability
- Panel, voltages, comp status
- Queryable across runs
Steps
Ten-step workflow checklist covering PBMC isolation through gated frequency export.
- Isolate, stain, wash, acquire
- Each tick timestamped
- Cytometer run auto-logged
Compounds
Antibody panel (CD3, CD4, CD8, CD45), viability dye, FACS buffer, and Ficoll pre-linked from the compound database.
- Antibody lots inline
- Titrated working dilutions
- Low-stock warnings before run
Links & Resources
Pre-wired to your lab's flow SOPs, panel validation document, and the FlowJo workspace for this study.
- PBMC Flow SOP v2.7
- Panel validation document
- FlowJo workspace linked
Storage & Files
Antibody aliquots, frozen PBMC vials, FCS exports, and FlowJo workspace files.
- 4 °C antibody storage
- Attachment slots labelled
- FCS + WSP ready on save
Use this template for your next flow panel.
Edit the configuration to match your panel and sample type, run the experiment from a tested baseline, and capture every gated frequency and compensation matrix in a structured record. Browse other templates built for the workflows real labs actually use.
Common questions
Can I configure the template for my panel and sample type?
Yes. Every section is editable. Swap in different fluorochrome panels (3-color through 18-color spectral), change the sample source (PBMC, whole blood, dissociated tumor, cell line), adjust the viability dye (Live/Dead Near-IR, Zombie Aqua, 7-AAD, PI), or change the cytometer model and laser configuration. Save your edits as a private template scoped to your lab, or publish back to the ELabELN template library.
Does the template handle compensation tracking?
The compensation matrix is recorded as part of the acquisition metadata. The template captures whether single-color compensation controls were run on the same day, the comp method used (auto or manual), and any spillover adjustments applied. Linking the FCS export and FlowJo workspace as attachments preserves the full audit trail for the gated analysis.
How does the template handle FMO controls?
FMO (fluorescence-minus-one) control samples are recorded as separate experiments linked to the panel run. The template includes a field for whether FMO boundaries were used and for which markers, supporting the typical immunophenotyping workflow where activation or rare-population markers need an FMO to set the positive gate threshold.
Is it included in every ELabELN plan?
Yes. Every published template in the ELabELN library is available to all ELabELN subscribers in both Standard and Suite editions, with unlimited users in either edition.
Can my whole lab use this template?
Yes. Every ELabELN edition includes unlimited users, so the PI, postdocs, grad students, rotating researchers, and visiting collaborators can all use the template without per-seat charges. Granular permissions let the PI control who can edit flow runs versus only review them.
How quickly can my lab start running flow in ELabELN?
ELabELN Standard cloud deployment is typically live in 1-2 days. Once the instance is provisioned, this template loads from the library in a single click, with the panel, sample source, and acquisition parameters editable to match the cytometer and protocol your lab actually runs.