Here we collect the information for the public regarding software parts of our project. E.g. examples that go with publications (Journal of Cystic Fibrosis,2021. https://doi.org/10.1016/j.jcf.2021.10.005). However we have more solutions lying around and are interested in adapting our solutions to new setups. So if you are interested in these feel free to contact us, we will find a way to help you.
Currently you will find the
- alignment script (ImageJ macro file), here
- recipe to create masks with Inkscape (e.g. well covers or manual bubble references); recorded as a video capture found here.
- "blue" stain version of the KNIME pipeline, using adaptive local thresholding and filtering by size and circularity, can be found here
- examples files here
Coming up soon will be
- more analysis pipelines and cohort collection scripts
- a version for clear / unstained bubble detection
Work in progress
- robust automated well edge detection
The same goes for potential hardware to use: we have a working setup, which was described here that we want to develop further and like to share. Thus developing it for and with the community.