Getting Started

This section of the documentation describes, in order, how to install starfish, gives a brief overview of starfish’s data model and its expectations for how data is formatted, provides an example of how to use starfish’s tools to construct the index used by starfish to interact with image data, provides instructions on loading and visualizing data, and jumps into a worked example of constructing and applying an example data processing pipeline.

• Data Model
  • Field of View
  • Processing Model
  • Dual Coordinate Systems
  • Next Steps
• 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
• Loading and Selecting Data
  • Visualizing Data
• Available datasets
• Example Data Processing Workflow
  • Using the API

# TODO ambrosejcarr: needs a comparison between smFISH and multiplex methods, otherwise later # statements don’t make any sense.

The following section Creating an Image Processing Pipeline goes into each of these sections in more detail.