Advanced BiofilmQ analysis pipelines: Curating, importing and analyzing single-cell segmentations скачать в хорошем качестве

Advanced BiofilmQ analysis pipelines: Curating, importing and analyzing single-cell segmentations

Advanced BiofilmQ analysis pipelines: Curating, importing and analyzing single-cell segmentations | Niklas Netter | October 18th, Halfway to I2K 2023 Authors: Niklas Netter, Biozentrum, University of Basel, Basel, Switzerland; Hannah Jeckel, California Institute of Technology, Pasadena, California, USA; Eva Jiménez-Siebert, Biozentrum, University of Basel, Basel, Switzerland; Knut Drescher, Biozentrum, University of Basel, Basel, Switzerland; Description: This workshop focuses on how to curate single-cell segmentation results in order to import them into BiofilmQ. We will use StarDist OPP as an example CNN-based segmentation and show how images can be converted into a format that is recognized as an external segmentation by BiofilmQ. After the import, we will go through some parameter calculation pipelines which are relevant specifically to single-cell segmented data. Note, that there will be two additional workshops for BiofilmQ: An introduction workshop, which can be attended prior to this one to learn or refresh the basics of BiofilmQ, as well as another advanced workshop covering channel merging and single-cell properties. Pre-Workshop Instructions: Please -         download and install BiofilmQ: https://biofilmq.readthedocs.io/en/la.... To ensure that you have the latest version, we recommend to update BiofilmQ about a week prior to the workshop -         install the StarDist OPP plugin in napari: https://merge-stardist-masks.readthed... If possible, use the Matlab-based BiofilmQ 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 and StarDist OPP. Feel free to explore the existing Tutorials on YouTube (   • Hannah Jeckel - BiofilmQ, a software tool ...  . Some basic familiarity with BiofilmQ is beneficial to attend this workshop. The workshop will cover the content of the following two tutorials: -         https://biofilmq.readthedocs.io/en/la... https://merge-stardist-masks.readthed... Keywords: BiofilmQ, StarDist OPP, spatiotemporal quantification