GitLab

this is the workflow to be used, e.g. with the example data the path is set to my home folder and has to be adjusted to fit to your machine, where you stored the example or your own files. The python extension has to be installed accordingly, if you run into trouble feel free to contact us and we will help you set this up. If installed correctly it will take the well definition and the _alin_ files found in the image folder and produce the other files found in the folder. Thus if you delete these they will be recreated in the same location otherwise overwritten.

example set of four time points with a sweat production, cholinerg stimulation in this case. With the folder structure for the pipeline example with the cholinerg mask next to the image folder. It contains the input as well as resulting masks and table with the count as well as scatter plots showing the bubble count, and size over the time points