sptx-format | Image data format specification for spaceTx

sptx-format is a Python library. sptx-format has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can download it from GitHub.

This document describes the spaceTx file format specification for image-based biological assays. The spaceTx format is designed to support the construction of a data tensor, which generalizes the approaches taken by sequential single-molecule FISH and assays that identify targets by building codes over multiple imaging rounds. Each of theses assays produce images that can form a data tensor. The data tensor contains a series of (x, y) planar image planes that represent specific z-planes, imaging channels (c), and imaging rounds (r). Together these form a 5-dimensional tensor (r, c, z, y, x) that serves as a general representation of an image-based transcriptomics or proteomics assay, and is the substrate of the starfish package. The goal of this repository is to define a self-describing data format that specifies how a set of 2-d images form a field of view, and specifies how multiple fields of view interact to form a larger experiment. The spaceTx format accomplishes this by combining these images, stored in 2-dimensional TIFF format, with a series of JSON files that describe how to organize each TIFF file into the 5-dimensional imaging tensor. Combined with imaging metadata and a pipeline recipe, both of which are defined elsewhere, these files enable a pipeline to generate the desired outputs of a spatial assay: a gene expression matrix augmented with spatial locations of transcripts and cells.