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BioImageFlow
BioImageFlow

Workflow Authors

  • Installation
  • Quick Start
  • Concepts
    • Architecture
    • Type System
    • Tools
    • Graph Construction
    • Execution
    • Caching and Provenance
  • Tutorials
    • Basic Workflow
    • Writing Custom Tools
    • Output Templating
    • Merge Strategies
    • Reusable and Nested Workflows
    • Parallelism
    • Cancellation
    • Shared Memory
    • Creating a Custom Tool Package
    • Tool Packaging and Versioning
  • Workflow Demos
    • FISH Spot Counting Per Nucleus
    • Exploring ATLAS Spot Detection Parameters
    • Benchmarking Nuclei Segmentation on BBBC038
    • Cell Counting and Phenotyping
    • Low-SNR Restoration
    • SAIRPICO Deconvolution
    • Live-Cell Migration Tracking

GUI / Platform Integrators

  • GUI / Platform Integrators
    • Overview
    • Wire Format
    • Loading: from_dict
    • WorkflowSession
    • ToolRegistry
    • Live Validation
    • Planning and Cache State
    • Disabled Nodes
    • Progress and Cancellation
    • Tool Schemas

Tool Packages

  • Tool Packages
  • bioimageflow-common-tools
    • Collect
    • Concat
    • ConnectedComponents
    • CrossJoin
    • ExtractChannel
    • Files
    • FilterTableRows
    • Generate
    • InnerJoin
    • JoinOnColumn
    • LabelOverlaps
    • Mosaic
    • SelectColumns
    • TableFromCsv
    • WriteTable
    • Common Glue Workflow
  • bioimageflow-io-tools
    • BioIOConvertImage
    • ConvertImageFormat
    • ConvertToOmeTiff
    • ConvertToOmeZarr
    • ReadImageMetadata
    • SelectChannel
    • SelectDimensions
    • SelectScene
    • SelectTimepoint
    • SelectZRange
    • ValidateImageLayout
  • bioimageflow-segmentation-tools
    • Cellpose3
    • CellposeSAM
    • DistanceWatershedSegment
    • FilterLabels
    • LocalThresholdSegment
    • nnInteractive
    • OtsuThresholdSegment
    • PostprocessLabels
    • SplitTouchingObjects
    • StarDistSegmenter
    • ThresholdSegment
    • WatershedSegment
    • BBBC038 Segmentation Benchmark Workflow
  • bioimageflow-measurement-tools
    • AggregatePerImage
    • CountLabels
    • DiceIoU
    • IntensityProperties
    • LabelBenchmark
    • NormalizeFeatures
    • ObjectMatchingMetrics
    • RegionProperties
    • ShapeProperties
    • SummarizeTable
    • Object Measurement Workflow
  • bioimageflow-spot-tools
    • AssignSpotsToLabels
    • AtlasSpotDetection
    • DetectSpots
    • FilterSpots
    • RenderSpots
    • SpotColocalization
    • SpotQualityMetrics
    • SpotSummary
    • SpotsToLabels
  • bioimageflow-tracking-tools
    • BTrackLink
    • FilterObjects
    • LabelsToObjects
    • TrackMetrics
    • TrackQualityMetrics
    • TrackSummary
    • TrackTableValidate
    • TracksToLabels
    • UltrackLink
  • bioimageflow-restoration-tools
    • BackgroundSubtract
    • CAREamicsPredict
    • GaussianDenoise
    • MedianDenoise
    • RestorationMetrics
    • RestoreImage
    • RichardsonLucyRestoration
    • UnsharpMask
  • BioImageFlow SAIRPICO Tools
    • CImgDenoising
    • GaussianPSF
    • GibsonLanniPSF
    • HotspotDetection
    • HotspotToSpots
    • MedianDenoising
    • RichardsonLucyDeconvolution
    • SpitfireDeconvolution
    • WienerDeconvolution

Reference

  • Reference
    • Errors
    • Logging
    • Environments
    • Testing Reference
    • Releasing Python Packages
    • Tool Package Release Contract
    • BioImageFlow Tool Package Strategy
    • Output and Cache Storage Specification
    • Agent Tool and Workflow Playbook
    • Unified workflow contract
    • API Reference
      • bioimageflow_core
      • bioimageflow
      • bioimageflow.validation
  • BioImageFlow Library Specifications
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Concepts¶

In-depth explanations of BioImageFlow’s design and internals.

  • Architecture
  • Type System
  • Tools
  • Graph Construction
  • Execution
  • Caching and Provenance
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Architecture
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Quick Start
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