Advanced BiofilmQ analysis and visualization

Advanced BiofilmQ analysis and visualization | Hannah Jeckel | October 19th, Halfway to I2K 2023 Authors: Hannah Jeckel, California Institute of Technology, Pasadena, California, USA; Eva Jiménez-Siebert, Biozentrum, University of Basel, Basel, Switzerland; Niklas Netter, Biozentrum, University of Basel, Basel, Switzerland; Knut Drescher, Biozentrum, University of Basel, Basel, Switzerland; Description: This workshop is aimed at BiofilmQ users who already have some experience using BiofilmQ or attended the introduction workshop. We will go through some advanced workflows such as merging of fluorescent channels, calculating user-defined parameters and performing batch processing. We will also explore the visualization tab in more detail by going through the different plotting options and additional features such as filtering/gating. Note, that there are two additional workshops for BiofilmQ at this conference: An introduction workshop as well as a workshop specifically dedicated to curating and importing single-cell segmentation data. You are welcome to attend several workshops. For new users, we recommend attending the introduction workshop prior to this one to learn or refresh the basics of BiofilmQ. Pre-Workshop Instructions: Please download BiofilmQ and the Sample data here: https://biofilmq.readthedocs.io/en/latest/usage/installation.html. To ensure that you have the latest version, we recommend that you update your BiofilmQ version one week prior to the workshop. If possible, use the Matlab-based version. If you do not have a Matlab license, you can use the .exe version. In this case, please install BiofilmQ prior to the workshop and open the sample data directory to ensure that it is working. If you encounter any issues, please reach out to us at least 3 days prior to the workshop, so that we can assist you in setting up BiofilmQ. Feel free to explore the existing Tutorials on YouTube (https://www.youtube.com/watch?v=hM3J7eHvcAA&list=PLzmiOL-opPEoo_Zyymcq0-WT4tevmiGhJ). Some basic experience with BiofilmQ is beneficial to follow this workshop. Keywords: Biofilm, Microbial Communities, Spatiotemporal quantification"