pytacs 2025.11.27

Pytacs: Python-implemented Topology-Aware Cell Segmentation for high-resolution spatial transcriptomics

Pytacs - Python-implemented Topology-Aware Cell Segmentation

Note: this is a prototype for DeTACH. Pytacs was initially a Python package but now supports command-line usage.

Copyright (C) 2025 Xindong Liu

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.

A tool for segmenting/integrating sub-cellular spots in high-resolution spatial transcriptomics into single-cellular spots and cell-type mapping leveraging paired scRNA-seq.

Requirements

It could be simply installed by pip install pytacs.

For conda users,

conda create -n pytacs python=3.12 -y
conda activate pytacs
pip install pytacs

For python3 users, first make sure your python is of version 3.12, and then in your working directory,

python -m venv pytacs
source pytacs/bin/activate
python -m pip install pytacs

For developers, requirements (at develop time) are listed in requirements.in (initial dependencies), requirements.txt (full dependencies) and requirements.tree.txt (for a tree view).

For developers using Poetry, the dependencies lock file is poetry.lock and the project information including main dependencies is listed in pyproject.toml.

To use it for downstream analysis in combination with Squidpy, it is recommended to use a seperate virtual environment to install Squidpy.

Usage

(Updated in 2025.11.27)

Pytacs now is packed as a commandline tool:

See help:

$ python -m pytacs -h

If you are interested in using Pytacs as a python package, we recommend using pytacs.recipe module. See docstring in pytacs.recipe.

Demo

Demo