Web-App for the detection of bioactive features in an untargeted metabolomics experiment with concomitant bioactivity determination.
The Web-App is based on streamlit and currently runs on the streamlit cloud service:
MicrospotReader can be installed on Windows and Linux. For installation on Linux please download the linux branch of this repository.
- Clone this repository
- Open Windows Terminal and go to the main folder of the repository:
cd <filepath>
- Create and activate a new conda environment:
conda env create -f environment.yml
conda activate microspotreader
- Start the App by running
run.py
A user guide for the WebApp is provided in the userguide-folder. It contains a walkthrough of each module of the app, a description of the algorithms used and an explanation of all possible settings as well as advice on how to set them.
Additionally, this Repository contains Jupyter Notebooks in the notebooks-folder if you do not wish to use the Web-App:
-
1_image_analysis.ipynb: Detection and analysis of MicroSpots as well as antimicrobial halos within an image. Determination of bioactivity. -
2_data_preparation.ipynb: Concatenation of Spot-Lists of the same LC-MS run and correlation of MicroSpots with a retention time. -
3_feature_finding.ipynb: Feature detection and annotation with activity data from .csv file prepared with previous steps and a .mzML file.