SpaceTx Format — starfish documentation
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      • 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
        • Quick Start
          • Quick Start
            • Prerequisites
            • Starfish Pipeline
        • Tutorials
          • 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
        • 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
        • 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.
        • 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
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          • SpotAttributes
          • Levels
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        • How can I contribute?
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      • About
        • Citing Starfish
        • License
  • SpaceTx Format

SpaceTx FormatΒΆ

  • 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