Biology session

Calcium is an important element of the animal body, therefore it is a highly researched topic. Often these studies involve monitoring calcium levels and analysing the results using computer programs. Selecting the regions of interests – also called ROIs – is a part of the process, which means selecting the areas to be investigated in the recording. However, the ROIs are determined manually, for which there is no standardised procedure, and their definition is hence subjective. Most of these programs are not available for free and their development has stopped, leading to obsolescence. The analysis process is not automated, their implementation is time consuming and human source demanding. It should be highlighted that they are not open-source programs, so it is not known what algorithms are used to deal with the data. Our goal was to develop an open-source, automated analysis program that is freely available to anyone and that uses objective methods to select the ROIs. The coding was done in the R programming language, one of the most used languages among biologists. Minimising the number of R packages used was an important aspect, partly because only a few packages are downloaded with R itself, the others are installed by the customer. Secondly, R is an open-source language so anyone can be a part of its development. The use of many packages increases the possibility that one of them will be updated, therefore changing the outcome of an already coded program. In addition, downloading the packages can be slow, which is less user friendly, and the reason for this is that R is a slower language. This caused difficulties at the beginning, as the size of the experimental data considerably increased the runtime of the code, but this has been improved over time. We were able to measure different types of polarised cells with the finished program. As there is no freely available open-source program like this currently, it will open up new opportunities for researchers. Our aim for the future is to translate this program into Python, another commonly used language in biology.