Tutorials and Examples

Quick Start

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

Data Formatting

Tutorials for converting data to SpaceTx Format.

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.

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.

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.

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