Running Multiple Pipelines
The Run multiple pipelines
dialog lets you select several pipelines
which will be run consecutively. Please note the following:
- CellProfiler 2.1 project files are not currently supported.
- Pipelines from CellProfiler 2.0 and lower are supported.
- If you want to use a pipeline made using CellProfiler 2.1, then you
need to include the project file list with the pipeline, by selecting Export >
Pipeline..., and under the "Save as type" dropdown, select "CellProfiler
pipeline and file list".
You can invoke Run multiple pipelines by selecting it from the file menu.
The dialog has three parts to it:
- File chooser: The file chooser lets you select the pipeline
files to be run. The Select all and Deselect all buttons to
the right will select or deselect all pipeline files in the list. The
Add button will add the pipelines to the pipeline list. You can add
a pipeline file multiple times, for instance if you want to run that pipeline
on more than one input folder.
- Directory chooser: The directory chooser lets you navigate to
different directories. The file chooser displays all pipeline files in the
directory chooser's current directory.
- Pipeline list: The pipeline list has the pipelines to be run in
the order that they will be run. Each pipeline has a default input and
output folder and a measurements file. You can change any of these by clicking
on the file name - an appropriate dialog will then be displayed. You can
click the remove button to remove a pipeline from the list
CellProfiler will run all of the pipelines on the list when you hit the