troutpy

Package for the analysis of unassigned RNA during segmentation in image-based spatial transcriptomics, in python.

Getting started

Please refer to the documentation, in particular, the API documentation.

Installation

You neeed to have Python 3.10 or newer installed on your system. If you don't have Python installed, we recommend installing Mambaforge.

There are several alternative options to install troutpy:

1. Install the latest release of troutpy from PyPI:

pip install troutpy

1. Install the latest development version:

pip install git+https://github.com/theislab/troutpy.git@main

Some functionality (spatial statistics, segmentation-free clustering, chord-diagram plots, morphological metrics, factor analysis, vendor-format readers) requires optional extras. Install everything with pip install "troutpy[all]", or pick individual extras (spatial-stats, segmentation-free, chord, morphology, factor-analysis, io, viz) as needed.

Usage

Please have a look at the Usage documentation and the tutorials.

import troutpy as tp

Reproducibility

Code, notebooks, and instructions to reproduce the results from the paper are available at the reproducibility repository. This repository also include diverse tutorials and compementary functions that are not core to Troutpy, but are required to reproduce the figures from Marco Salas et al. 2025.

Release notes

See the changelog.

Contact

For questions and help requests, you can reach out in the scverse discourse. If you found a bug, please use the issue tracker.

Citation

t.b.a