Usage

Software

Run gui.py in fluidics_v2_firmware_software/software to start the GUI

MERFISH

To run MERFISH sequences, load a .csv file and click 'Run Selected Sequences'. merfish-experiment.csv is an example.

After running the named operation, the syringe pump will extract liquid from the port in column 'fill_tubing_with' to fill the tubing. Setting the port value to '0' will disable this behavior.

Change configurations in config.json as needed.

• "serial_number" of microcontroller and syringe pump: Connect one serial device at a time and run list_controllers.py to find out the serial number.
• "valve_ids_allowed": Connect the selector valves to the ports on the PCB. If there are three selector valves, connect them to port 0, 1 and 2 and set "valve_ids_allowed" to [0, 1, 2].
• "tubing_fluid_amount_ul": Fluid in the tubings that connect each selector valve. This will be used for calculate the amount of fluid extracted in 'fill_tubing_with'.
• "reagent_name_mapping": Show the reagent names of each port in the GUI (optional).