Instrument PC
BFLOW-RCC1-TRAM-R1.fcsBD LSRFortessa · Annexin V / PI
protocol v9EXP-042operatorraw source
The biological data platform for wet-lab R&D
From instrument to publication. One platform.
EpistaBase captures instrument output automatically, keeps every run, analysis, and figure connected, and gives your team purpose-built scientific apps and code in one governed workspace.
automatic capture
analysis without downloads
full provenance
Instrument console
RUN COMPLETE
3,000 events
BFLOW-RCC1-TRAM
Annexin V / PI
Annexin V / PI
One workspace for the complete experimentreal product capture · 18 Aug 2026
Automatic capturesource: /exports/runs
The problem is not the raw file
The file survives. The experiment around it doesn’t.
A run moves from an instrument PC into desktop software, spreadsheets, email, and slides. The file may remain. The protocol, parameters, decisions, and path to the result quietly separate from it.
Desktop analysis
apoptosis_gate_v6.wspFlow workspace · local copy
gate treeparametersprotocol v9operator
Spreadsheet
apoptosis_final_v3.xlsxpopulation statistics · attachment
valuesgate treeparameterssource link
Slide deck
Figure 3B · apoptosiscopied visual · no live source
protocolanalysis versionsource datadecision history
What disappears between transfers
protocol versionexcluded eventsgate settingsanalysis historysource relationship
With EpistaBase, the context travels with the work
ProtocolExperimentRunDatasetAnalysisFigure
One continuous record
The record builds itself as the work happens.
Start with the protocol, capture the completed run automatically, analyze it where it lands, and keep every shared or published result connected to its source.
01 / CAPTURE
Capture automatically
Connect an instrument export folder so completed runs move into EpistaBase without a flash drive or manual upload.
source: BD LSRFortessa
destination: governed record
destination: governed record
02 / CONNECT
Attach the context
The original file lands with its protocol, experiment, run, instrument, operator, checksum, and access policy.
EXP-042 · protocol v9
SHA-256 verified
SHA-256 verified
03 / ANALYZE
Analyze without export
Gate flow data, inspect microscopy, fit curves, or run code directly against the same governed dataset.
Annexin V / PI mapped
notebook linked
notebook linked
04 / SHARE
Share the connected result
Send a controlled workspace link. Collaborators see the result, analysis state, and source—not another detached attachment.
viewer access
version: Draft (Live)
version: Draft (Live)
05 / REPRODUCE
Publish with provenance
Publish a frozen result with its source analysis, query log, and lineage preserved for review or reuse.
Frozen · v1.0.0
lineage secured
lineage secured
Scientific apps on the same data
Analyze where the data already lives.
Open governed datasets directly in purpose-built scientific apps or code. Every gate, annotation, parameter, and output returns to the experiment record.
Governed data layer
Connected to source data
Every instrument file, one browser.
Search across experiments, inspect source metadata, and trace any result back to the raw file that produced it.
- Automatic format detection and metadata extraction
- Search by experiment, instrument, file type, or date
- Raw source preserved with full activity history
Live product capture
MicroscopyPlate reader & 4PLqPCR / dPCRDensitometryReactive notebooks
Purpose-built scientific apps
Specialist tools. One connected record.
Flow cytometry, molecular biology, notebooks, microscopy, and code operate on the same governed data objects. Analysis no longer severs the source, permissions, or history.
Flow cytometry
Flow gating that continues past the plot.
Draw polygon gates, build population hierarchies, and import FlowJo workspaces. Then use those populations in code, figures, and controlled review without another export.
Familiar analysisPolygon gates, transforms, gate trees, and population statistics.
Connected outputGates and populations remain linked to the raw .fcs source.
Browser collaborationReview the same gate state instead of emailing workspace files.
Code-readyMove from a gated population into custom analysis on-platform.
Molecular biology
Construct maps that stay connected to the experiment.
Move between circular and linear views of a validated 7,784 bp construct while annotations, parts, and experimental context remain attached.
Sequence and mapSwitch views without losing annotations or feature identity.
Validated statusKeep construct state visible beside the scientific record.
Connected partsTrace promoters, coding regions, and tags within one workspace.
Experiment contextUse the same construct record across protocols and runs.
Connected lab notebook
The narrative stays connected to the work.
Write the scientific account with live links to protocols, experiments, analyses, and figures instead of reconstructing those relationships afterwards.
First-class linksReference governed records instead of pasting file paths.
Shared narrativeKeep decisions and interpretation beside the underlying work.
Reopen the sourceMove from a result back into the protocol, dataset, or analysis.
Connected scientific context
Every object knows what it belongs to.
A protocol belongs to an experiment. Runs and samples produce governed data. Apps or code produce analyses. Figures and reports retain the path back to every source.
Method
Drug treatment · v3.2
published protocol snapshot
Experiment
EXP-042 · Trametinib
question + execution record
Run
RUN-FLOW-014
Annexin V / PI acquisition
Data
BFLOW-RCC1-TRAM.fcs
3,000 events · Annexin V / PI
Analysis
Apoptotic cells · gate v6
1,341 / 3,000 events
Output
Figure 3B · apoptosis
embedded in summary report
Run
RUN-IMG-006
RCC1 · 24 Z-planes
Data
RCC1_TRAM_24h.czi
2048 × 2048 · 3 channels
Analysis
Caspase-3 ROI set · v4
42 regions · channel mixer
Output
Figure 4A · caspase-3
published image artifact
Run
RUN-PLATE-021
CellTiter-Glo · 96 wells
Data
viability_luminescence.csv
parsed table · 8.6 KB
Analysis
dose_response_v12.py
4PL fit · reactive notebook
Output
IC50 curve · 0.42 nM
figure + query log + report
FLOW ROUTE Protocol v3.2 → Experiment EXP-042 → RUN-FLOW-014 → raw .fcs → gate v6 → Figure 3B → report
One experiment, end to end
Every figure keeps a path home.
The same identity follows data through capture, analysis, review, and publication. Reopen a result and see the source, parameters, code, and history that made it.
Live product capture
Figure → analysis → source table
A published dose-response figure opens as a three-object lineage chain, with every derived-from edge and selected asset still inspectable.
3 objects · 2 derived-from edges
source: viability_luminescence.csv
selected asset metadata remains visible
Raw instrument file
The untouched .fcs export and its checksum are the permanent source record.
BFLOW-RCC1-TRAM-R1.fcssha256: 7e4c…9a12
Apps or code
Gates, transforms, notebooks, parameters, and derived values remain attached.
FSC-A / FSC-Hnotebook: analysis-v12
Publication figure
The visual is generated from live governed data instead of copied into a slide.
Figure 3Btwo-tailed t-test · p = 0.0012
Controlled review
Share the live result with explicit access instead of sending another detached file.
viewer access · controlled linkversion: Draft (Live)
Frozen record
Publish to preserve the figure artifact, source analysis, query log, and lineage as a frozen version.
Frozen · v1.0.0audit trail secured
Governance throughout
Data custody
Scoped agents
Useful to scientists. Safe for the organization.
Your data stays contained. Access stays scoped.
EpistaBase is designed for customer-controlled deployment, project- and dataset-scoped access, and durable attribution across human and automated work.
Discuss your deploymentMake the lab’s work queryable—with provenance attached.
Let agents query the records they are allowed to see. Answers retain the experiment, protocol, dataset, and analysis context needed to inspect the result.
Talk about governed agents
Start with one instrument workflow
Keep the path from run to result intact.
Bring a real instrument workflow. See how EpistaBase can capture its output, support the analysis, and preserve the complete record through collaboration and publication.