Introduction to BiofilmQ: File import, threshold-based cube segmentation and basic parameter calcs

Introduction to BiofilmQ: File import, threshold-based cube segmentation and basic parameter calculations | Eva Jiménez-Siebert | October 17th, Halfway to I2K 2023

Authors: Eva Jiménez-Siebert, Biozentrum, University of Basel, Basel, Switzerland;
Hannah Jeckel, California Institute of Technology, Pasadena, California, USA;
Niklas Netter, Biozentrum, University of Basel, Basel, Switzerland;
Knut Drescher, Biozentrum, University of Basel, Basel, Switzerland;

Description: This workshop serves as an introduction (or refresher) to BiofilmQ. We will cover how to import different image file types, perform basic image segmentation and the in-built cube declumping. We will also go through some of the most common segmented-image parameter calculations, data export and visualization.
Note, that there will be two additional workshops for BiofilmQ, covering more advanced topics including single-cell parameter calculations introduced in the latest update. You are welcome to attend more than one workshop.

Pre-Workshop Instructions: Please download BiofilmQ and the Sample data here: https://biofilmq.readthedocs.io/en/la.... 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 (   • Hannah Jeckel - BiofilmQ, a software ...  , however this is not a prerequisite as we will cover similar topics in this workshop.

Keywords: Biofilm, Microbial Communities, Spatio-temporal quantification