Help & Reference — starfish documentation
  • Installation
  • User Guide
  • Examples
  • API
  • More
      • Installation
        • Using virtual environments
        • Installing starfish
        • Installing starfish on Windows
        • Jupyter notebook
        • Installing starfish in development mode
      • User Guide
        • Formatting Data
        • 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
        • Working with starfish outputs
        • Processing at Scale with AWS
        • Further Reading
          • Working with Starfish Outputs
            • 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
          • 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
      • Tutorials and Examples
        • Quick Start
        • Data Formatting
        • Data Formatting Examples Using TileFetcher
        • Data Loading
        • Tutorials
        • How Tos
        • Example Pipelines
          • 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
              • Convert structured data into SpaceTx Format
              • Output directory contents
              • Merge outputs by modifying experiment.json
              • Don’t forget to replace the fake codebook.json
              • Load up the experiment
            • Formatting with TileFetcher
              • Create some synthetic data to form into a trivial experiment.
              • Directory contents
              • Define FetchedTile subclass
              • Define TileFetcher subclass
              • Run write_experiment_json()
              • Don’t forget to replace the fake codebook.json
              • Load up the experiment
          • Data Formatting Examples Using TileFetcher
            • 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
          • Data Loading
            • Loading Data
              • Loading Experiments
              • Loading Fields of View
              • Loading Images
            • 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.
          • Tutorials
            • Image Registration
            • Illumination Correction
              • Prospective Correction
              • Retrospective Correction
            • Removing Autofluorescence
              • Clipping
              • White Top-Hat Filtering
            • 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 FindSpotsAlgorithm
            • Watershed Segmentation
            • Example of Custom Watershed Pipeline
            • Pre-defined Watershed Segmentation Pipeline
          • How Tos
            • Visualizing Data
              • Start with the quick start tutorial
              • Using the GUI
              • Adding additional layers
              • Naming your layers with napari commands
              • Directly visualizing SpotFindingResults
            • 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
            • Processing sequential smFISH in 3D
              • Define image filters
              • Define a spot detection method
              • Construct the pipeline
              • Load data & run pipeline
            • STARmap processing example
              • Visualize raw data
              • Visualize the codebook
              • Registration
              • Equalize channel intensities
              • Find spots
              • Decode spots
            • Reproduce published osmFISH results with starfish
              • Load Data into starfish from the cloud
              • Filter and visualize data
              • Decode the processed data into spatially resolved gene expression
              • Compare to pySMFISH peak calls
            • Reproduce published MERFISH results with starfish
              • Load Data
              • Visualize codebook
              • Visualize raw data
              • Filter and scale raw data before decoding into spatially resolved gene expression
              • Visualize processed data
              • Decode the processed data into spatially resolved gene expression profiles
              • Compare to results from paper
              • Visualize results
            • BaristaSeq Processing Workflow
              • Load Data
              • Select one plane
              • Register the data
              • Project into 2D
              • Correct Channel Misalignment
              • Remove Registration Artifacts
              • Correct for bleed-through from Illumina SBS reagents
              • Remove image background
              • Scale images to equalize spot intensities across channels
              • Detect Spots
            • Reproduce DARTFISH results with starfish
              • Load Data
              • Visualize codebook
              • Visualize raw data
              • Filter and scale raw data before decoding into spatially resolved gene expression
              • Decode the processed data into spatially resolved gene expression profiles
              • Compare to benchmark results
              • Visualize results
              • Parameter and QC analysis
      • Help & Reference
        • Data Model
          • Field of View
          • Processing Model
          • Dual Coordinate Systems
          • Next Steps
        • SpaceTx Format
          • SpaceTx Image Format Specification
            • Introduction
            • Format Specification
            • Experiment
            • Manifest
            • Field of View
            • Codebook
          • JSON Schemas
            • Validation
              • Usage
              • Examples
        • Available datasets
        • 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
        • SpaceTx Consortium
          • Pipelines
        • Request Support
      • API
        • Data Structures
          • Experiment
            • Experiment
              • Experiment.fov()
              • Experiment.fovs()
              • Experiment.fovs_by_name()
              • Experiment.from_json()
              • Experiment.items()
              • Experiment.keys()
              • Experiment.values()
              • Experiment.verify_version()
          • Field of View
            • FieldOfView
              • FieldOfView.get_image()
              • FieldOfView.get_images()
          • ImageStack
            • ImageStack
              • ImageStack.apply()
              • ImageStack.axis_labels()
              • ImageStack.export()
              • ImageStack.from_numpy()
              • ImageStack.from_path_or_url()
              • ImageStack.from_tilefetcher()
              • ImageStack.from_tileset()
              • ImageStack.from_url()
              • ImageStack.get_slice()
              • ImageStack.isel()
              • ImageStack.log
              • ImageStack.map()
              • ImageStack.max_proj()
              • ImageStack.num_chs
              • ImageStack.num_rounds
              • ImageStack.num_zplanes
              • ImageStack.raw_shape
              • ImageStack.reduce()
              • ImageStack.sel()
              • ImageStack.sel_by_physical_coords()
              • ImageStack.set_slice()
              • ImageStack.shape
              • ImageStack.tile_metadata
              • ImageStack.tile_shape
              • ImageStack.to_multipage_tiff()
              • ImageStack.transform()
              • ImageStack.xarray
          • Codebook
            • Codebook
              • Codebook.code_length
              • Codebook.decode_metric()
              • Codebook.decode_per_round_max()
              • Codebook.from_code_array()
              • Codebook.from_numpy()
              • Codebook.get_partial()
              • Codebook.item()
              • Codebook.open_json()
              • Codebook.searchsorted()
              • Codebook.synthetic_one_hot_codebook()
              • Codebook.to_json()
              • Codebook.zeros()
          • ExpressionMatrix
            • ExpressionMatrix
              • ExpressionMatrix.item()
              • ExpressionMatrix.load()
              • ExpressionMatrix.save()
              • ExpressionMatrix.save_anndata()
              • ExpressionMatrix.save_loom()
              • ExpressionMatrix.searchsorted()
          • IntensityTable
            • IntensityTable
              • IntensityTable.concatenate_intensity_tables()
              • IntensityTable.from_image_stack()
              • IntensityTable.from_spot_data()
              • IntensityTable.get_log()
              • IntensityTable.has_physical_coords
              • IntensityTable.item()
              • IntensityTable.open_netcdf()
              • IntensityTable.searchsorted()
              • IntensityTable.synthetic_intensities()
              • IntensityTable.to_features_dataframe()
              • IntensityTable.to_netcdf()
              • IntensityTable.zeros()
            • transfer_physical_coords_to_intensity_table()
          • DecodedIntensityTable
            • DecodedIntensityTable
              • DecodedIntensityTable.from_intensity_table()
              • DecodedIntensityTable.item()
              • DecodedIntensityTable.searchsorted()
              • DecodedIntensityTable.to_decoded_dataframe()
              • DecodedIntensityTable.to_expression_matrix()
              • DecodedIntensityTable.to_mermaid()
          • BinaryMaskCollection
            • BinaryMaskCollection
              • BinaryMaskCollection.from_binary_arrays_and_ticks()
              • BinaryMaskCollection.from_external_labeled_image()
              • BinaryMaskCollection.from_fiji_roi_set()
              • BinaryMaskCollection.from_label_array_and_ticks()
              • BinaryMaskCollection.from_label_image()
              • BinaryMaskCollection.mask_regionprops()
              • BinaryMaskCollection.open_targz()
              • BinaryMaskCollection.to_targz()
              • BinaryMaskCollection.uncropped_mask()
          • LabelImage
            • LabelImage
              • LabelImage.from_label_array_and_ticks()
              • LabelImage.log
              • LabelImage.open_netcdf()
              • LabelImage.to_netcdf()
              • LabelImage.xarray
        • slicedimage
          • ImageFormat
          • numpy_writer()
          • tiff_writer()
        • Data Formatting
          • Converting Structured Data
            • format_structured_dataset()
          • Tile Fetcher Interface
            • FetchedTile
              • FetchedTile.coordinates
              • FetchedTile.extras
              • FetchedTile.shape
              • FetchedTile.tile_data()
            • TileFetcher
              • TileFetcher.get_tile()
            • write_experiment_json()
        • Image Manipulation
          • Filtering
            • Bandpass
              • Bandpass.run()
            • Clip
              • Clip.run()
            • ClipPercentileToZero
              • ClipPercentileToZero.run()
            • ClipValueToZero
              • ClipValueToZero.run()
            • DeconvolvePSF
              • DeconvolvePSF.run()
            • ElementWiseMultiply
              • ElementWiseMultiply.run()
            • GaussianHighPass
              • GaussianHighPass.run()
            • GaussianLowPass
              • GaussianLowPass.run()
            • IlastikPretrainedProbability
              • IlastikPretrainedProbability.import_ilastik_probabilities()
              • IlastikPretrainedProbability.run()
            • Laplace
              • Laplace.run()
            • LinearUnmixing
              • LinearUnmixing.run()
            • Map
              • Map.run()
            • MatchHistograms
              • MatchHistograms.run()
            • MeanHighPass
              • MeanHighPass.run()
            • Reduce
              • Reduce.run()
            • WhiteTophat
              • WhiteTophat.run()
            • ZeroByChannelMagnitude
              • ZeroByChannelMagnitude.run()
          • Learn Transform
            • Translation
              • Translation.run()
          • Apply Transform
            • Warp
              • Warp.run()
          • Segmentation
            • Watershed
              • Watershed.run()
        • Spots
          • Detecting Pixels
            • PixelSpotDecoder
              • PixelSpotDecoder.run()
          • Finding Spots
            • BlobDetector
              • BlobDetector.image_to_spots()
              • BlobDetector.run()
            • FindSpotsAlgorithm
              • FindSpotsAlgorithm.run()
            • LocalMaxPeakFinder
              • LocalMaxPeakFinder.image_to_spots()
              • LocalMaxPeakFinder.run()
            • TrackpyLocalMaxPeakFinder
              • TrackpyLocalMaxPeakFinder.image_to_spots()
              • TrackpyLocalMaxPeakFinder.run()
          • Decoding Spots
            • CheckAll
              • CheckAll.run()
            • DecodeSpotsAlgorithm
            • MetricDistance
              • MetricDistance.run()
            • PerRoundMaxChannel
              • PerRoundMaxChannel.run()
            • SimpleLookupDecoder
              • SimpleLookupDecoder.run()
          • Target Assignment
            • AssignTargetsAlgorithm
              • AssignTargetsAlgorithm.run()
            • Label
              • Label.run()
        • Morphology Transformations
          • Binarize
            • ThresholdBinarize
              • ThresholdBinarize.run()
          • Filter
            • AreaFilter
              • AreaFilter.run()
            • Map
              • Map.run()
            • MinDistanceLabel
              • MinDistanceLabel.run()
            • Reduce
              • Reduce.run()
          • Merge
            • MergeAlgorithm
            • SimpleMerge
              • SimpleMerge.run()
          • Segment
            • WatershedSegment
              • WatershedSegment.run()
        • Types
          • Coordinates
            • Coordinates
              • Coordinates.X
              • Coordinates.Y
              • Coordinates.Z
          • Physical Coordinates
            • PhysicalCoordinateTypes
              • PhysicalCoordinateTypes.X_MAX
              • PhysicalCoordinateTypes.X_MIN
              • PhysicalCoordinateTypes.Y_MAX
              • PhysicalCoordinateTypes.Y_MIN
              • PhysicalCoordinateTypes.Z_MAX
              • PhysicalCoordinateTypes.Z_MIN
          • Axes
            • Axes
              • Axes.CH
              • Axes.ROUND
              • Axes.X
              • Axes.Y
              • Axes.ZPLANE
          • Features
            • Features
              • Features.AREA
              • Features.AXIS
              • Features.CELLS
              • Features.CELL_ID
              • Features.CODEWORD
              • Features.CODE_VALUE
              • Features.DISTANCE
              • Features.GENES
              • Features.INTENSITY
              • Features.PASSES_THRESHOLDS
              • Features.SPOT_ID
              • Features.SPOT_RADIUS
              • Features.TARGET
          • SpotAttributes
            • SpotAttributes
              • SpotAttributes.empty()
              • SpotAttributes.required_fields
              • SpotAttributes.save_geojson()
          • Levels
            • Levels
              • Levels.CLIP
              • Levels.SCALE_BY_CHUNK
              • Levels.SCALE_BY_IMAGE
              • Levels.SCALE_SATURATED_BY_CHUNK
              • Levels.SCALE_SATURATED_BY_IMAGE
        • Validation
          • Validators
            • SpaceTxValidator
              • SpaceTxValidator.validate_file()
              • SpaceTxValidator.validate_object()
          • Helpers
            • validate()
            • validate_file()
          • Error messages
        • Utilities
          • Configuration
            • StarfishConfig
              • StarfishConfig
            • environ
              • environ
          • Provenance Logging
            • Example
        • Interactive Image Viewer: display()
          • display()
        • Plotting Utilities
          • diagnose_registration()
          • imshow_plane()
          • intensity_histogram()
          • overlay_spot_calls()
        • Datasets
          • BaristaSeq()
          • DARTFISH()
          • ISS()
          • ImagingMassCytometry()
          • MERFISH()
          • MOUSE_V_HUMAN()
          • STARmap()
          • SeqFISH()
          • allen_smFISH()
          • osmFISH()
      • 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
  • Help & Reference

Help & Reference¶

  • Data Model
  • SpaceTx Format
  • Available datasets
  • Configuration
  • Glossary
  • SpaceTx Consortium
  • Request Support