segtraq 0.0.4

SegTraQ - A Python toolkit for quantitative and visual quality control of segmentation and transcript assignment in spatial omics data.

SegTraQ

⚠️ 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 under 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.

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