SpaceTx File Format


The SpaceTX File Format is designed to describe one or more tensors along with a codeboook to decode detected spots into targets. The documentation for the format can be found here.

Converting Data to SpaceTx Format

We provide three types of tools to convert data into SpaceTx-Format. One is a Bio-Formats writer which writes SpaceTx-Format experiments using the Bio-Formats converter. Bio-Formats can read a variety of input formats, so might be a relatively simple approach for users familiar with those tools.

Second, we provide a mechanism by which the user organizes the data as 2D tiles with a clearly defined filename schema, and a conversion tool. There is documentation and an example for that mechanism.

If neither of these models fit, then we provide a generalized mechanism where conversion is managed through a set of interfaces where the user provides python code responsible for obtaining the data corresponding to each 2D tile. Example formatters for a variety of datasets are also available. This same interface can also be used to directly load data, although there may be performance implications in doing so.