➰ Loopy Browser

Loopy Browser is a performant visualization tool for spatial transcriptomics experiments.

Usage

Head over to https://loopy-browser.pages.dev/ to see the Loopy Browser with example data.

Data Preparation

All data must be processed prior to being used in the Loopy Browser.

Installation

git clone https://github.com/chaichontat/loopy-browser/
conda env create -n loopy -f loopy-browser/environment.yml
conda activate loopy
conda install jupyter jupyterlab
pip install ./loopy-browser

An example script is available at scripts/run_sample.ipynb. This is run using a Jupyter notebook. To start, run jupyter lab at the cloned directory.

Nomenclature

Being compatible with static hosting, there are multiple layers of data.

• sample.json: this contains the overall detail of the sample, such as its names and list of features.
• {features}.json: these are either headers for ChunkedJSON or headers and data for PlainJSON.