UnifiedFlowInfrastructure for Evidence

Research / Calcium imaging

Calcium imaging.From regions
to relationships.

We build calcium imaging workflows for region selection, trace extraction, and network exploration. Researchers can inspect the methods, parameters, and quality-control decisions behind the analysis.

Discuss your calcium workflow ↗Explore the approach ↓
Regions, activity and relationships: three connected analysis planesCell regions, activity traces and a network view on three connected analysis planes.01 / REGIONSFIELD / ROI01Regions02 / ACTIVITYABCTIME →02Activity03 / RELATIONSHIPS03Relationships

Before the analysis

The image has
a history.

Retain the microscope and detector setup, indicator, frame timing, and spatial scale with each recording. These acquisition details help researchers assess region morphology and interpret fluorescence dynamics.

  • Instrument & optics
  • Indicator & preparation
  • Frame timing & spatial scale
See how the setup stays connected

From the platform

Three planes.
One connected workflow.

Image analysis, event-level activity and network exploration, brought together around your research.

01 / ROI plane

Start with the regions.

Identify regions in the image and keep each one connected to its trace.

  • Field of view
  • Region review
  • Extracted traces
A calcium image field labeled A, B and C, with matching enlarged region crops and fluorescence traces.
An image field, three region details and their matching traces.

02 / Event plane

Make activity visible.

Connect fluorescence traces to inferred calcium events, with the timing available to explore.

  • Calcium traces
  • Inferred events
  • Activity over time
Three fluorescence traces with matching inferred event markers and an aligned event raster for regions A, B and C.
Three regions, their traces and inferred events in one ten-second window.

03 / Network plane

See how activity relates.

Explore functional coactivity across regions and bring the wider pattern into view.

  • Coactivity views
  • Network relationships
  • Shared time windows
The actual eight-region coactivity graph and its matching binary connectivity matrix; A is highlighted consistently.
The same regional relationships shown as a network and a connectivity matrix.
About these figures

Adapted from an existing platform recording. Image pixels, trace samples, inferred event times and graph connections are retained. Labels and styling are adapted for presentation.

Network links show functional coactivity within the selected window. These examples demonstrate workflow capabilities; they do not establish biological findings or imply lab endorsement.

Methods & orchestration

Your methods, connected.
Your runs, accounted for.

Connect specialist imaging tools in a configured pipeline, from microscopy files to reviewable outputs. Retain processing parameters, intermediate artifacts, and QC decisions so your team can inspect each step.

Calcium Scientific v2Six connected processing groups

  1. Workflow

    Define the method

    Stage dependencies, processing backends and expected outputs.

  2. Parameter profile

    Tune for the preparation

    ROI criteria, background correction, decay time and event thresholds.

  3. Run record

    Retain the execution

    Resolved settings, source references and the artifacts each stage produced.

  1. 01

    Prepare the recording

    Preflight → register → ingest

    Check source metadata, establish dataset identity and materialize the movie while preserving the original input.

    Retained outputSource manifest + canonical movie
    Technique & settings

    ND2, TIFF, and AVI are declared inputs. Retain timing metadata and frame selections with the recording; the workflow profile determines how the source is prepared.

    • Source timing
    • Initial-frame trim
    • Source identity
  2. 02

    Stabilize the movie

    Bounded native motion correction

    Estimate frame shifts with phase correlation and carry the alignment record into downstream processing.

    Retained outputCorrected movie + shift history
    Technique & settings

    The native motion path records frame shifts, correction parameters and motion metrics. Its bounded entrypoint supports a separate motion run before post-motion processing.

    • Shift bounds
    • Frame selection
    • Motion output reference
  3. 03

    Build the region set

    Cellpose + CaImAn → candidate fusion

    Bring morphology and CNMF-derived candidates together, retaining masks and the evidence behind each region.

    Retained outputCandidate masks + region evidence
    Technique & settings

    The post-motion implementation invokes Cellpose and CaImAn CNMF initialization, then combines candidate masks with native morphology processing. Candidate generation is distinct from accepting a cell.

    • Area & shape criteria
    • Inter-region spacing
    • Candidate backends
  4. 04

    Extract. Inspect. Refine.

    Mask-based extraction + ROI review

    Connect raw fluorescence, background-corrected traces and ΔF/F to cell labels and merge decisions.

    Retained outputTraces + reviewed-mask handoff
    Technique & settings

    The v2 profile includes annular and shared-background correction. The reviewed path finalizes a snapshot of scientist decisions before re-extracting traces from reviewed masks; configured automated ROI review is also supported.

    • Background strategy
    • ROI decisions
    • Finalized review snapshot
  5. 05

    Estimate the activity

    Reference OASIS → event analysis

    Apply calcium deconvolution and evaluate candidate events alongside signal quality and trace evidence.

    Retained outputInferred activity + event tables
    Technique & settings

    The reviewed downstream path uses reference OASIS AR(1), with decay time, baseline and event thresholds recorded in its settings. Inferred activity remains an estimate for scientific review.

    • Calcium decay time
    • Baseline method
    • Event threshold
  6. 06

    Keep the work reusable

    Quality summary → package → archive

    Package figures, tables, manifests, and run parameters together so researchers can trace the outputs to the processing that produced them.

    Retained outputReview bundle + provenance + receipts
    Technique & settings

    Packaging collects analysis artifacts and provenance. The export stage records checksums and destination receipts; the configured output set determines what is delivered. Figure tooling includes Matplotlib for static exports.

    • Review outputs
    • Artifact manifest
    • Archive destination

The connection is the infrastructure.

A stage produces the inputs for the next. Profiles carry the method choices; run records carry what happened. A finalized ROI review can feed a downstream run that reuses the motion-corrected movie.

Explore run provenance ↗Where the workflow runs ↗

Tools within the workflow

Based on the current Calcium Scientific v2 workflow and its bounded processing paths. Steps are grouped for readability; enabled backends and delivered outputs depend on the run configuration.

Scientists in the workflow

Your judgment.
Part of the process.

Review on desktop or mobile, keep the reasons with the evidence, and make each review useful for the next round of work.

A detailed view of a calcium review bundle with image regions and matching traces; a mobile ROI card with left/right decisions, reason capture and separate merge review; activity notes and a saved decision record. A clearly labeled proposed cohort session compares student and PI judgments. A separate pathway selects review evidence for dataset curation and model evaluation.
Review the evidence. Record the judgment. Build on what your team learns.

Research operations

Keep a batch of recordings moving.

Carry the source movies, region sets, traces and review decisions forward with the method and settings used. Keep that record useful for the next experiment, method comparison or researcher joining the lab.

Working with bulk fluorescence? Explore fiber photometry ↗

A conversation, grounded in your work

Discuss your calcium imaging workflow.

Tell us about the preparation, the current analysis, and where your lab needs support.

Discuss your workflow