Metadata-Version: 2.1
Name: ficture
Version: 0.0.1.post3
Summary: Segmentation free factor analysis for sub-micron resolution spatial transcriptomics
Author-email: Yichen Si <ycsi@umich.edu>
License: CC BY-NC 4.0
Project-URL: Homepage, https://github.com/seqscope/ficture
Project-URL: Bug Tracker, https://github.com/seqscope/ficture/issues
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: geopandas
Requires-Dist: scipy
Requires-Dist: scikit-learn
Requires-Dist: joblib
Requires-Dist: matplotlib
Requires-Dist: Pillow
Requires-Dist: Jinja2
Requires-Dist: opencv-python
Requires-Dist: shapely
Requires-Dist: geojson
Requires-Dist: torch
Requires-Dist: pymde
Requires-Dist: ete3
Requires-Dist: PyQt5

# FICTURE

*This repository is under active construction*

FICTURE: Scalable segmentation-free analysis of sub-micron resolution spatial transcriptomics

[preprint](https://biorxiv.org/cgi/content/short/2023.11.04.565621v1)

## General usage
```
ficture <command> <args>
```
Type `ficture` to see the list of available commands.

## Installation

Create a virtual environment and install dependencies
```
pip install -r requirements.txt
```
Install
```
pip install ficture
```

## Example - Simulated data
See `./examples/simulation.md` for a complete example including simulating a high reoluation dataset, running FICTURE, and evaluating the result.


## Example - Real data
See `./examples/realdata.md` for commands of processing an example data in `./examples/data/`. The data a subset from a public [Vizgen MERSCOPE mouse liver dataset](https://info.vizgen.com/mouse-liver-access) (mouse liver 1 slice 1).
