ISS Decoding Pipeline

This repositor provides instructions for setting up and installing a simple decoding pipeline for in situ sequencing. This repository mainly contains tools used by Wahlby group (Uppsala University) for decoding in situ sequencing data.

Getting Started

Make sure you have Conda or Miniconda installed on your system.

Setting Up Conda Environment

Run the following commands from a terminal (Linux/Mac) or command prompt (Windows):

Create conda environtment with Python 3.10

conda create -y -n isstools python=3.10

Activate the conda environment:

conda activate isstools

In the activated environment, install the dependencies:

conda install -y -c conda-forge numpy scipy matplotlib networkx scikit-image=0.19 scikit-learn "tifffile>=2023.3.15" zarr pyjnius blessed

These dependencies are necessary for Ashlar, a Python package for image stitching and registration.

Run the following command to install Ashlar:

pip install ashlar

Finally, install additional dependencies:

pip install pandas pillow torch psfmodels tqdm

We recommend using TissUUmaps for visualization and quality control.

Usage

Now that you have set up the environment and installed the required packages, you're ready to use the pipeline. See the notebook tutorial.ipynb for usage.