ST Spot Detector
A web tool for automatic spot detection and positional adjustments for ST datasets.
The arrays used to generate ST datasets may contain positional variations due to printing artifacts. This web tool aims to detect correct spot positions using the images generated from the ST protocol. In order to obtain relevant experimental data, it is also possible to automatically select the spots which are located under the tissue, using a corresponding HE image. The spot positions and selections are further adjustable to one's own needs. A file is generated which contains the corrected spot coordinates of the ST data as adjusted array coordinates and pixel coordinates as well as file containing a 3x3 affine matrix to transform array coordinates to pixel coordinates which can be useful for downstream analysis.
The following packages are required:
Python 3.6+ Node.js 10.0+ npm 6.0+
Additionally, the ST tissue recognition library needs to be installed.
A modern browser is required for the front-end interface. The web app has been tested on Chrome 66 and Firefox 60.
If you want to deploy the ST Spot detector locally on your computer you can use this singularity container. Otherwise follow the deployment instructions below.
Clone the repository
git clone https://github.com/SpatialTranscriptomicsResearch/st_spot_detector.git
Move into the directory
Install the dependencies
Create and activate a Python virtual environment
pip install virtualenv virtualenv venv source venv/bin/activate
Install the dependencies in requirements.txt.
cd server pip install -r requirements.txt
Install the tissue recognition library (still within the Python virtual environment). Follow the instructions here.
Build the client side files:
cd ../client npm install make dist
Run the server with the following command:
cd ../server python -m app
The server is WSGI-compatible and can, alternatively, be run with a WSGI server of your choice.
Optional. It may be desirable to configure port-forwarding to be able to access the web tool through port 80, e.g. using iptables:
sudo iptables -t nat -A PREROUTING -p tcp --dport 80 -i eth0 -j DNAT --to 0.0.0.0:8080
For any queries or concerns, feel free to contact the authors at the addresses given below.
If you want to cite the ST Spot detector:
ST Spot Detector: a web-based application for automatic spot and tissue detection for Spatial Transcriptomics image data sets DOI: 10.1093/bioinformatics/bty030
For a guide on using the ST spots detection tool, please refer to this guide.
MIT (see LICENSE).
Kim Wong firstname.lastname@example.org
Ludvig Bergenstråhle email@example.com
Jose Fernandez firstname.lastname@example.org