MicroSpot Reader

Web-App for the detection and quantification of Spots on a microfluidics device for the determination of bioactivity of HPLC-fractions in parallel to an HPLC-MS experiment.

Web-App

The Web-App is based on streamlit and currently runs on the streamlit cloud service:

Local Installation:

1. Clone this repository
2. Open Windows Terminal and go to the main folder of the repository:

cd <filepath>

1. Create and activate a new conda environment:

conda env create -f environment.yml

conda activate uspotreader

4. Start the App by running the following command:

streamlit run MicrospotReader_App.py

Jupyter Notebooks

Additionally, this Repository contains Jupyter Notebooks in the notebooks-folder if you do not wish to use the Web-App:

• image_analysis.ipynb: Detection and analysis of MicroSpots as well as antimicrobial halos within an image. Determination of bioactivity.

• data_preparation.ipynb: Concatenation of Spot-Lists of the same LC-MS run and correlation of MicroSpots with a retention time.

• mzml_annotation.ipynb: Annotation of MS1 spectra within a .mzML file with bioactivity at the corresponding retention time.

• feature_finding.ipynb: Feature detection and annotation with activity data from .csv file prepared with previous stepas and a .mzML file.