Tutorials and Examples¶

Quick Start¶

Tutorial introducing first-time users to a full starfish pipeline.

Quick Start

Data Formatting¶

Tutorials for converting data to SpaceTx Format.

Format Structured Data

Formatting with TileFetcher

Formatting with :py.TileFetcher

Data Formatting Examples Using TileFetcher¶

There is currently no widely used standard data format for image-based microscopy data. starfish works best when data is converted into the SpaceTx data format. Here, we provide several examples of how to convert data from non-standardized data formats into SpaceTx format from a variety of types of input data shapes and sizes, demonstrating the flexibility of TileFetcher.

These examples are provided for illustrative purposes, demonstrating how the TileFetcher is used in practice. They will need to be adapted to meet the specific needs of your data.

Format BaristaSeq

Format In Situ Sequencing Mouse x Human Experiment

Format In-Situ Sequencing Data

Format Imaging Cytof Data

Data Loading¶

There are two ways to load experiment data into starfish. The standard method requires data to be in SpaceTx Format with an experiment.json file. The advanced method uses TileFetchers to load data from any file format into starfish.

Loading Data

Loading Data through TileFetchers

Tutorials¶

Tutorials for the image processing steps that construct a starfish pipeline

Image Registration

Illumination Correction

Removing Autofluorescence

Loading ImageJ ROI Sets

Image Manipulations

Normalizing Intensity Values

Pixel-Based Decoding

Using ilastik in starfish

Assigning Spots to Cells

Normalizing Intensity Distributions

Spot-Based Decoding

Watershed Segmentation

How Tos¶

How Tos for using starfish classes, methods, and functions

Visualizing Data

Finding Spots with LocalMaxPeakFinder

Finding Spots with :py.LocalMaxPeakFinder

Plotting Intensity Distribution

Showing Image of ImageStack Plane

Finding Spots with TrackpyLocalMaxPeakFinder

Finding Spots with :py.TrackpyLocalMaxPeakFinder

Decoding Spots with SimpleLookupDecoder

Decoding Spots with :py.SimpleLookupDecoder

Clipping

Finding Spots with BlobDetector

Finding Spots with :py.BlobDetector

Clipping Value To Zero

Decoding Spots with PerRoundMaxChannel

Decoding Spots with :py.PerRoundMaxChannel

Assessing SpotFindingResults

Assessing :py.SpotFindingResults

When to Use Each TraceBuildingStrategies

Clipping Percentile To Zero

Matching Histograms

Decoding Spots with MetricDistance

Decoding Spots with :py.MetricDistance

Example Pipelines¶

Starfish pipelines tailored for image data generated by groups using various image-based transcriptomics assays. When adapting these examples for other data sets, be cognizant that pipelines must be designed for the imaging system properties, sample characteristics, as well as the assay used.

ISS Processing Workflow

Processing sequential smFISH in 3D

STARmap processing example

Reproduce published osmFISH results with starfish

Reproduce published MERFISH results with starfish

BaristaSeq Processing Workflow

Reproduce DARTFISH results with starfish

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