mintflow

MintFlow (Microenvironment-induced and INtrinsic Transcriptomic FLOWs) is a package to generate disentangled microenvironment-induced and intrinsic gene expression vectors from spatial transcriptomics data. It interoperates with the scverse ecosystem to enable seamless analysis workflows of spatial transcriptomics data.

Installation

Install MintFlow via pip:

pip install mintflow

For more detailed instructions, visit our documentation.

It's highly recommended to setup wandb when training your own MintFlow models.

To do so:

Go to wandb and create an account.
Create a project called "MintFlow".

Resources

An installation guide, tutorials and API documentation is available in the documentation.
Please use issues to submit bug reports.
If you would like to contribute, check out the contributing guide.
If you find MintFlow useful for your research, please consider citing the MintFlow manuscript.

Reference

@article{Akbarnejad2025,
  author    = {Akbarnejad, A. et al.},
  title     = {Mapping and reprogramming microenvironment-induced cell states in human disease using generative AI},
  journal   = {bioRxiv},
  year      = {2025},
  doi       = {10.1101/2025.06.24.661094},
  url       = {https://doi.org/10.1101/2025.06.24.661094}
}

Development Status
- 3 - Alpha
Intended Audience
- Science/Research
Natural Language
- English
Operating System
- POSIX :: Linux
Programming Language
- Python :: 3.10
- Python :: 3.11
Topic
- Scientific/Engineering :: Bio-Informatics

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