SegTraQ

⚠️ On July 28th, 2026, the history of this repository was rewritten to reduce its size. If you cloned the repo before this date and intend to contribute to this project, please create a fresh clone to avoid any conflicts!

⚠️ Note: SegTraQ is under active development. Features, interfaces, and functionality may change in upcoming releases. SegTraQ currently supports imaging-based spatial transcriptomics data only. Support for sequencing-based spatial transcriptomics is in development and will be included in a future release. To install the latest development version, run pip install git+https://github.com/LazDaria/SegTraQ.

SegTraQ (Segmentation and Transcript Assignment Quality Control) is a Python toolkit for quantitative and visual quality control of segmentation and transcript assignment in spatial omics data.

Getting Started

Please refer to the documentation for details on the API and tutorials.

Installation

To install SegTraQ, first create a python environment and install the package using

pip install segtraq

The installation of the package should take less than a minute.

Configuration

The number of CPU cores used by SegTraQ can be set globally via segtraq.settings.n_jobs or individually for each metric using the n_jobs parameter. By default, SegTraQ uses one core (n_jobs=1).

import segtraq as st

st.settings.n_jobs = -1  # Use all available CPU cores

System Requirements

Hardware Requirements

SegTraQ requires only a standard computer with enough RAM to support the in-memory operations.

Software Requirements

SegTraQ depends on the following packages:

scanpy
spatialdata
geopandas
rtree
rasterio
squidpy
anndata
ovrlpy