|
|
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)
|
|
|
- recipe to create masks with Inkscape (e.g. well covers or manual bubble references)
|
|
|
- "blue" stain version of the KNIME pipeline, using adaptive local thresholding and filtering by size and circularity
|
|
|
- alignment script ([ImageJ](https://imagej.net/software/fiji/) macro file), [here](https://gitlab.gwdg.de/mnieter1/autobusted/-/tree/master/Image%20Alignment)
|
|
|
- recipe to create masks with [Inkscape](https://inkscape.org/) (e.g. well covers or manual bubble references); recorded as a video capture found [here](https://gitlab.gwdg.de/mnieter1/autobusted/-/tree/master/Inkscape).
|
|
|
- "blue" stain version of the KNIME pipeline, using adaptive local thresholding and filtering by size and circularity, can be found [here](https://gitlab.gwdg.de/mnieter1/autobusted/-/tree/master/KNIME%20workflows)
|
|
|
- examples files can be found [here](https://gitlab.gwdg.de/mnieter1/autobusted/-/tree/master/example_files)
|
|
|
|
|
|
Coming up soon will be
|
|
|
- more analysis pipelines and cohort collection scripts
|
... | ... | |