API — starfish documentation
  • Installation
  • User Guide
  • Examples
  • API
  • More
      • Installation
        • Using virtual environments
        • Installing starfish
        • Installing starfish on Windows
        • Jupyter notebook
      • User Guide
        • Loading Data
        • Manipulating Images
        • Correcting Images
        • Enhancing Signal & Removing Background Noise
        • Normalizing Intensities
          • Whether to normalize
          • How to normalize
            • Normalizing Intensity Distributions
            • Normalizing Intensity Values
        • Finding and Decoding Spots
          • Spot-Based Decoding
          • Pixel-Based Decoding
          • What Decoding Pipeline Should I Use?
        • Segmenting Cells
          • Thresholding and Watershed
          • Manually Defining Cells
          • Machine-Learning Methods
        • Assigning Spots to Cells
        • Assessing Performance Metrics
        • Other Utilities
        • Feature Identification and Assignment
      • Examples
        • Feature Identification
        • Segmenting Cells
        • Assigning Spots to Cells
        • Tissue Corrections
        • Removing autofluorescence
          • Clipping
        • Image Registration
        • Image Corrections
        • Illumination Correction
        • Chromatic Aberration
        • Deconvolution of Optical Point Spread Functions
          • Learning the PSF from image data
        • Example Image Correction Pipeline
        • Loading ImageJ ROI Sets
        • Image Manipulations
        • Cropping
          • Crop on Load
          • Selecting Images
        • Projection
        • Normalizing Intensity Values
        • Pixel-Based Decoding
        • Using ilastik in starfish
        • Calling Out to ilastik Trained Pixel Classifier
        • Loading ilastik Probability Map
        • Transforming Probability Map to Masks
        • Assigning Spots to Cells
        • Normalizing Intensity Distributions
        • Spot-Based Decoding
          • Spot Finding
          • Trace Building
          • Spot Decoding
          • Comparison of FindSpotsAlgorithms
        • Watershed Segmentation
        • Example of Custom Watershed Pipeline
        • Pre-defined Watershed Segmentation Pipeline
        • Quick Start
          • Quick Start
            • Prerequisites
            • Starfish Pipeline
        • Data Formatting
          • Format Structured Data
            • Create some synthetic data to form into a trivial experiment.
            • Directory contents
            • Contents of coordinates.csv
            • Construct an experiment out of the raw files.
            • List the output directory
            • Load up the experiment
          • Format BaristaSeq
          • Format In Situ Sequencing Mouse x Human Experiment
          • Format In-Situ Sequencing Data
          • Format Imaging Cytof Data
          • Format MERFISH data
          • Format SeqFISH Data
          • Format osmFISH Data
          • Format STARmap data
        • Advanced Data Loading
          • Loading Data through TileFetchers
            • Create some synthetic 5D data
            • Write as a series of 3D tiffs.
            • Now build a FetchedTile and TileFetcher based on this data.
            • Load the data as an ImageStack.
        • How Tos
          • Finding Spots with LocalMaxPeakFinder
          • Plotting Intensity Distribution
          • Showing Image of ImageStack Plane
          • Finding Spots with TrackpyLocalMaxPeakFinder
          • Decoding Spots with SimpleLookupDecoder
          • Clipping
          • Finding Spots with BlobDetector
          • Clipping Value To Zero
          • Decoding Spots with PerRoundMaxChannel
          • Assessing SpotFindingResults
          • When to Use Each TraceBuildingStrategies
          • Clipping Percentile To Zero
          • Matching Histograms
            • How to match histograms across channels
            • How to match histograms across channels and rounds
            • How to match histograms across z-planes
            • Risk of using MatchHistograms inappropriately
          • Decoding Spots with MetricDistance
        • Example Pipelines
          • ISS Processing Workflow
          • Single Field of View for sequential single-molecule FISH processed in 3d
            • Define image filters
            • Define a spot detection method
            • Construct the pipeline
            • Load data, run pipeline, display results
      • Help & Reference
        • Starfish Usage
          • Starfish Usage Checklist
          • Data Files and Formats
            • Data and Auxiliary Images
            • Codebook
          • Data Pre-processing
            • Data should be pre-registered and if the assay is code-based, the transformation should be applied
            • Data should be corrected for optical aberrations
            • No other processing should be applied to the data
        • Data Model
          • Field of View
          • Processing Model
          • Dual Coordinate Systems
          • Next Steps
        • SpaceTx Format
          • Input Data Formats
            • SpaceTx Image Format Specification
              • Introduction
              • Format Specification
              • Experiment
              • Manifest
              • Field of View
              • Codebook
            • JSON Schemas
          • Output Formats
            • IntensityTable
              • Data
              • Table Metadata
              • Feature Metadata
              • Implementation
              • Serialization
            • ExpressionMatrix
              • Data
              • Metadata
              • Implementation
              • Serialization
            • DecodedSpots
              • Required Columns
              • Optional Columns
              • Implementation
              • Serialization
            • SegmentationMask
              • Implementation
              • Serialization
        • SpaceTx File Format
          • Overview
          • Converting Data to SpaceTx Format
        • Advanced data formatting
          • Example Data Conversion
          • Downloading Data
          • Formatting single-plane TIFF files in sptx-format
          • Creating a Build Script
        • Validation
          • Usage
          • Examples
        • Loading and Selecting Data
          • Visualizing Data
        • Available datasets
        • Example Data Processing Workflow
          • Using the API
        • Working with Starfish Outputs
        • Processing With AWS
          • Prerequisites
          • Set up your data
            • Upload your Data
            • Create a Recipe File
          • Set up your Batch Jobs
            • Create a custom IAM Role
            • Register your Jobs
          • Run your Batch Jobs
        • Configuration
          • Default values
          • Main environment variables
            • STARFISH_CONFIG
            • STARFISH_VALIDATION_STRICT
            • STARFISH_VERBOSE
          • Backend environment variables
            • SLICEDIMAGE_CACHING_SIZE_LIMIT
            • SLICEDIMAGE_CACHING_DIRECTORY
            • SLICEDIMAGE_CACHING_DEBUG
        • Glossary
        • Request Support
      • API
        • Data Structures
          • Experiment
          • Field of View
          • ImageStack
          • Codebook
          • ExpressionMatrix
          • IntensityTable
          • DecodedIntensityTable
          • BinaryMaskCollection
          • LabelImage
        • Image Manipulation
          • Filtering
          • Learn Transform
          • Apply Transform
          • Segmentation
        • Spots
          • Detecting Pixels
          • Finding Spots
          • Decoding Spots
          • Target Assignment
        • Morphology Transformations
          • Binarize
          • Filter
          • Merge
          • Segment
        • Types
          • Coordinates
          • Physical Coordinates
          • Axes
          • Features
          • SpotAttributes
          • Levels
        • Validation
          • Validators
          • Helpers
          • Error messages
        • Utilities
          • Configuration
            • StarfishConfig
            • environ
          • Provenance Logging
            • Example
        • Datasets
      • Developer Guide
        • How can I contribute?
        • Installing starfish for developers
        • Creating a new algorithm for an existing pipeline_component
        • Reporting bugs
        • Code contributions
        • Notebook contributions
        • Debugging Errors
        • Upgrading to a new version
        • Reporting bugs
      • About
        • Citing Starfish
        • License
  • API

APIΒΆ

  • Image Manipulation
    • Filtering
    • Learn Transform
    • Apply Transform
    • Segmentation
  • Spots
    • Detecting Pixels
    • Finding Spots
    • Decoding Spots
    • Target Assignment
  • Morphology Transformations
    • Binarize
    • Filter
    • Merge
    • Segment
  • Types
    • Coordinates
    • Physical Coordinates
    • Axes
    • Features
    • SpotAttributes
    • Levels
  • Validation
    • Validators
    • Helpers
    • Error messages
  • Utilities
    • Configuration
      • StarfishConfig
      • environ
    • Provenance Logging
      • Example
  • Datasets