Segmentation free factor analysis for sub-micron resolution spatial transcriptomics

Project description

FICTURE

This repository is under active construction

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

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 (mouse liver 1 slice 1).

Project details

Release history Release notifications | RSS feed

0.0.3.1

May 20, 2024

0.0.3

Apr 17, 2024

0.0.2

Apr 4, 2024

This version

0.0.1.post3

Nov 15, 2023

0.0.1.post2

Nov 15, 2023

0.0.1

Nov 14, 2023

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