ImageJ tool for percentage estimation of pneumonia in lungs

The software tool is developed on demand of Radiological Department of Faculty Hospital of Královské Vinohrady, with the aim to provide a tool to estimate the percentage of pneumonia (or COVID-19 presence) in lungs. Paper Estimation of Covid-19 lungs damage based on computer tomography images analysis presenting the tool is available on F1000reserach DOI: 10.12688/f1000research.109020.1. The underlying dataset is published in Zenodo (DOI:10.5281/zenodo.5805939). One of the challenges was to design a tool that would be available without complicated install procedures and would process data in a reasonable time even on office computers. For this reason, 8-bit and 16-bit version of the tool exists. The FIJI software (or ImageJ with Bio-Formats plugin installed) was selected as the best candidate. Examples of use and tutorials are available at GitHub. 

Underlying data:
DOI:10.5281/zenodo.5805939
The first five datasets are analyzed using this tool, with results and parameters to repeat the analysis in results_csv.csv or results.xlsx.

Contributions:
Martin SCHÄTZ:       Coding, tool testing, data curation, data set analysis
Olga RUBEŠOVÁ:    Code review, tutorial preparation, tool testing, data set analysis
Jan MAREŠ:             Tool testing, data set analysis
Alan SPARK:             Tool testing

The work was funded by the Ministry of Education, Youth and Sports by grant ‘Development of Advanced Computational Algorithms for evaluating post-surgery rehabilitation’ number LTAIN19007. The work was also supported from the grant of Specific university research – grant No FCHI 2022-001.