Method Recipe¶
There are 6 basic actions to build a recipe.
1. PORT: port name (string)¶
Valve switches to specified port.
PORT: water
2. PUMP: pump volume in uL (integer)¶
Syringe pump draws specified volume through flowcell lane.
PUMP: 2000
2. TEMP: temperature in degrees Celsius (float)¶
Set temperature of flowcell.
TEMP: 55.0
3. HOLD: hold time in min. (integer)¶
Recipe pauses for specified time. The recipe can also be paused until user input by using STOP instead of an integer.
HOLD: 10
4. WAIT: IMAG or port name (string)¶
Recipe waits to continue until the other flowcell is imaging (IMAG) or switches to port name. If there is only one flowcell, WAIT is ignored.
WAIT: water
5. IMAG: z focal planes (integer)¶
The flowcell is imaged at the specified number of z focal planes at the sections listed in the experiment config.
IMAG: 15
Example Recipe¶
This recipe automates a method called 4i. In the 4i method config the variable reagents and first port are set as follows:
variable reagents = 1stab, 2ndab first port = blockingThe 4i method stains tissue sections by first blocking sections for 1 hr, then staining sections with 1stab, followed by 2ndab for 2 hrs. After the sections are imaged in imaging buffer, antibodies are eluted off the tissue sections, and are then ready for subsequent rounds of staining.
PORT: water #Move valve to water wash (port 2) PUMP: 2000 #Pump 2000 uL PORT: elution #Move valve to elution (port 3) PUMP: 500 #Pump 500 uL HOLD: 10 #Hold for 10 minutes PUMP: 500 #Pump 500 uL HOLD: 10 #Hold for 10 minutes PUMP: 500 #Pump 500 uL HOLD: 10 #Hold for 10 minutes PUMP: 500 #Pump 500 uL HOLD: 10 #Hold for 10 minutes PUMP: 500 #Pump 500 uL HOLD: 10 #Hold for 10 minutes PUMP: 500 #Pump 500 uL HOLD: 10 #Hold for 10 minutes PORT: blocking #Move valve to blocking buffer (port 4) PUMP: 800 #Pump 800 uL HOLD: 60 #Hold for 60 min PORT: PBS #Move valve to PBS wash (port 1) PUMP: 2000 #Pump 2000 uL PORT: 1stab #Move valve to primary antibody (variable) PUMP: 500 #Pump 500 uL HOLD: 120 #Hold for 120 min PORT: PBS #Move valve to PBS wash (port 1) PUMP: 2000 #Pump 2000 uL PORT: 2ndab #Move valve to secondary antibody (variable) PUMP: 500 #Pump 500 uL HOLD: 120 #Hold for 120 min PORT: PBS #Move valve to PBS wash (port 1) PUMP: 2000 #Pump 2000 uL WAIT: water #Wait till other flowcell is washing with water PORT: imaging #Move valve to imaging buffer (port 5) PUMP: 750 #Pump 750 uL IMAG: 15 #image 15 z sections