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Getting started

After folowing the experimental protocol, we provide the openst python package for transforming the raw sequencing data into objects that can be used for spatial, single-cell analysis.

More specifically, our pipeline consists of the following steps:

  1. Preprocessing of sequencing
  2. Preprocessing of imaging
  3. Align image to transcriptome: the spatial coordinates of transcripts are aligned to the imaging modality.
  4. Generating a cell-by-gene matrix: transcripts are quantified per cell using the segmentation information.
  5. 3D reconstruction of tissue imaging and transcriptome from serial sections. We provide tutorials for interactive visualization of 3D data.

If you're familiar with Python, you can install openst with pip, the Python package manager. If not, we recommend using docker.

Installation

The computational tools of the Open-ST workflow are published as a Python package and can be installed with pip, ideally by using a virtual environment. Open up a terminal and install openst with:

pip install openst

Tip

If you don't have prior experience with Python, we recommend reading Using Python's pip to Manage Your Projects' Dependencies, which is a really good introduction on the mechanics of Python package management and helps you troubleshoot if you run into errors.

with docker

The official Docker image is a great way to get up and running in a few minutes, as it comes with all dependencies pre-installed. Open up a terminal and pull the image with:

docker pull rajewsky/openst

The openst executable is provided as an entry point and serve is the default command.

You can run a terminal for openst by running 

docker run -it openst

Optionally, you might want to enable X11 redirection to enable GUI support (e.g., for the openst manual_pairwise_aligner_gui tool). Follow these steps:

  1. Install X Server on your host machine if not already installed.
  2. Allow connections to your X Server by running the following command on your host: 
    xhost +
  3. Run the Docker container with the following additional options: 
    docker run -it --rm -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix openst

Now, you can execute PyQt5-based applications, and the GUI will be displayed on your host machine.

Note

  • Ensure that the X Server on your host allows connections (xhost +) before running the container,
  • Make sure the necessary dependencies are installed on your host machine for PyQt5 applications.
  • Remember to close the X Server connections after using the container: 
    xhost -

with git

openst can be directly used from GitHub by cloning the repository into a subfolder of your project root which might be useful if you want to use the very latest version:

git clone https://github.com/rajewsky-lab/openst.git

Next, install the theme and its dependencies with:

pip install -e openst