Laura Wiggins, PhD student in Biology

Email: l.wiggins@sheffield.ac.uk

Open

_{^ Summary of the CellPhe toolkit, taken from publication in Nature Communications. © the authors, 2023. Licensed under a Creative Commons Attribution 4.0 International Licence.}

This case study shows how open research approaches can be used when developing a new toolkit - CellPhe. This toolkit was initially developed using three different programming languages, but to make it more openly accessible, it was later developed using R, a universally accessible programming language, to broaden the user base of the toolkit. Additionally, to ensure that anyone could use this toolkit, regardless of their research or programming background, a written manual and demonstration video was published to guide users through installation and usage of the toolkit. These resources were trialled by non-experts in a useful exercise which helped to shape the toolkit based on user feedback. All code, data, and user guides are freely available on GitHub.

CellPhe is a toolkit for the characterisation of cellular phenotypes from time-lapse images. It is freely available to install as an R package and is complemented by a user-friendly GUI that can be accessed using an internet browser. The open-source nature of CellPhe was of utmost importance during its development, hence great efforts were made to ensure CellPhe was easy to use and easy to access. Originally, the CellPhe toolkit was written in three separate programming languages, taking advantage of the strengths of each language, though this pipeline restricted easy use of CellPhe to only macOS users as well as those with programming experience. The researchers therefore sought to develop CellPhe into an R package so that all stages from their previous workflow would be fully integrated into just one language, making it universally accessible for all operating systems. Though this integration was challenging, the researchers note that it was also extremely worthwhile as it immediately broadened the user base of our tool.

As well as this, the researchers wanted to ensure that CellPhe would be able to be used and understood by researchers of all backgrounds, irrespective of their programming background. They therefore published a manual that guides the user through installation and usage of the CellPhe R package, with a worked example to demonstrate its use on a real data set. Furthermore, the researchers published a demonstration video to exemplify the use of the CellPhe GUI on a worked example. During the development stages, researchers asked a non-expert microscopist to trial both the R package and the GUI by following the provided user manual and demonstration video. The researchers note that this was a hugely useful exercise and helped them to shape the toolkit and additional resources, showing the value in seeking and acting upon user feedback during tool development. All code, data and user guides are available in a CellPhe GitHub repository to allow others to reproduce all results included within the CellPhe publication and to interact with codes and parameters to suit their own analysis needs.

Though ensuring full transparency and openness of the toolkit required additional time and effort, as well as collaboration with RSEs, this resulted in software that is accessible to a much broader user base and in turn can be used for a wider variety of applications. This project gave the researchers the opportunity to discuss open research principles with inspiring researchers within the field and find ways that CellPhe could complement and build upon their established, open-source cell segmentation and tracking software. Through this process the researchers comment that they gained a huge appreciation for the concept of FAIR principles for research software, which was noted as a desirable trait within academic career advancement.

• Publication in Nature Communications: https://www.nature.com/articles/s41467-023-37447-3

• CellPhe press release: https://www.york.ac.uk/news-and-events/news/2023/research/new-tool-could-change-how-we-see-cells/

• Judges' and Peoples' Choice winner in York 3MT 2022: https://www.york.ac.uk/research/events/three-minute-thesis/2022/

Except where otherwise noted copyright in this work belongs to the author(s), licensed under a Creative Commons Attribution-NonCommercial 4.0 International License