RunPack is a microfluidic valving and microscope control suite designed for HT-MEK experiments using a variety of device layouts and configurations and extensible to multiple assay types and experimental workflows. It provides hardware control of Nikon Ti microscopes via MicroManager (MMCore) and WAGO-controlled solenoid-actuated pneumatic valving. This suite sits atop the FordyceLab AcqPack to integrate logging, scripting, and image acquisition into one framework.
- io: High-level classes for software and hardware control
- Experimental hardware access provided via the HardwareInterface, which allows for instantiation, control, and removal of connections to the microscope/camera/stage/sola, the WAGO, and temperature/humidity probes.
- Experimental details including device features, general assay parameters, and logging—managed by the ExperimentalHarness
- imagingcontrol: Collection of functions for imaging at single or multiple stage positions (rastered, multi-dimensional acquisitions), for single or multiple timepoints (kinetic)
- valvecontrol: Collection of basic valve-control functions with error checking and logging
- assays: High-level classes to execute a single device assay, a linear series of assays, or multi-device scheduled assays
- An HT-MEK-specific Assay class to introduce substrate and execute imaging
- An AssaySeries parent class for sequential assay execution
- (In development) A general-purpose task-scheduling "Riffled" Assay class for simultaneous/staggered assay execution using shared hardware (camera/scope/stage)
- mitomiprotocols: HT-MEK-specific experimental protocols/scripts
- config.json: A JSON configuration file specifying hardware parameters, software configuration, and experimental intial values
- valvemap.csv: A comma-delimited file specifying valve names corresponding to specific WAGO-controlled solenoids
- Check package requirements: use
pipreqson directory containing runpack - Install:
pip install -e git+https://github.com/FordyceLab/RunPack.git#egg=runpack- Note
-emakes package editable
- Note
- Register venv with Jupyter:
python -m ipykernel install --user --name=runpack - Enable GUI:
jupyter nbextension enable --py widgetsnbextension- Should resolve "Widget Javascript not detected" error