def movetoch4():
fluidics.stop_flow()
stage.move_to("J1")
stage.move_to("Ch1")
setpressure(0.1)
fluidics.open(1, 2, 3, 4, 6)
reset_force()
print("setup should be ready to go")
def false_positive(): #1 if it was ok, 0 if false positive
fluidics.close(1, 2, 3, 4, 5, 6)
gohome()
pause(0.8)
reset_force()
trap.move_by(dx=5, speed=6)
f1 = trap2.current_force
trap.move_by(dx=5.5, speed=6)
f2 = trap2.current_force
trap.move_by(dx=-10.5, speed=6)
print(" -FP" + str(round(f1, 2)) + " to " + str(round(f2, 2)))
if f2 > (4 * f1):
return 1
else:
return 0
def themainloop(
): #will return 1 if caught, 0 if attempted 60 times and failed
#check for beads first
bt = beadtest()
fluidics.close(1, 2, 3, 4, 5, 6)
if bt == 0:
setpressure(0.3)
fluidics.open(1, 2, 3, 6)
stage.move_to("beads")
catch_beads(86)
else:
#turn on fluidics
fluidics.open(1, 2, 3, 6)
# set up the pressure
stage.move_to("buffer")
setpressure(0.4)
#set traps at initial position and reset force
gohome()
reset_force()
print("initialized position")
caught = pingpongforce2()
attempts = 1
#moving into dna channel and starting pingpong
while caught != 1:
print(" we've attempted " + str(attempts) + " times")
#print(" new force ="+str(round(pforce,2)))
stage.move_to("DNA")
pause(dnadwell)
stage.move_to("buffer")
pause(dnadwell)
caught = pingpongforce2()
if attempts == 15:
return 0
if (attempts % 10) == 0:
pressurecycle()
attempts += 1
else:
attempts += 1
print("hopefully we finished")
return 1
def is_single_tether(max_force=70, min_force=30, backward_speed=1):
# min_forcce depemds on the rate of flow, especially when you have flow
# make sure that you don't have bubbles inside the system
trap1, trap2 = traps[:2]
distance = timeline["Distance"]["Distance 1"]
goto_distance(10)
print("traps are 10 um apart")
trap1.move_by(dx=-3, speed=backward_speed) # MAYBE play with this
reset_force()
pause(0.5) # MAYBE play with this
baseline_force = trap1.current_force
# print('baseline force')
# print(baseline_force)
trap1.move_by(dx=3, speed=5) # MAYBE play with this
force_list = []
ii = 0
# while distance.latest_value < 26: # MAYBE play with this, not sure how long you can stretch DNA
while ii < 38: # MAYBE play with this, not sure how long you can stretch DNA
ii += 1
trap1.move_by(dx=0.5, speed=5)
# print('trap1 force')
# print(trap1.current_force)
current_force = abs(baseline_force - trap1.current_force)
# print(current_force)
force_list.append(current_force)
if current_force > max_force:
print("Multiple tethers found")
return 2
# elif distance.latest_value > 16:
elif ii > 18:
if current_force > min_force:
# print('stdev of past 10 forces')
# print(std(force_list[-10:]))
if std(force_list[-10:]) < 2:
print("Single tether potentially found")
trap1.move_by(dx=-16, speed=5)
return 1
print("No tethers found")
trap1.move_by(dx=-16, speed=5)
return 0
def thelooploop(): #return 1 if done
chk = 0
while chk == 0:
print("starting loop loop")
chk = themainloop()
if chk == 1:
chk = false_positive()
else:
target_traps = traps[:2]
target_traps[1].clear()
target_traps[0].clear()
#hopefully caught something, move to buffer channel and reset all
stage.move_to("buffer")
gohome()
fluidics.stop_flow()
reset_force()
print("in the buffer channel with all reset")
#0 for no ssDNA, 1 for good, 2 for failed to pull
if makessDNA == 1:
print("time to try for ssDNA")
s = 0
while s != 1:
s = ssDNAstretch()
if s == 0:
setpressure(0.3)
fluidics.open(3, 6)
target_traps = traps[:2]
target_traps[1].clear()
target_traps[0].clear()
fluidics.close(3, 6)
return s
if s == 2:
continue
else:
return 1
def fish_for_dna(min_distance_um, max_distance_um, force_threshold_pN):
"""Oscillate between min and max distance while the force is under the threshold value"""
stage.move_to("DNA")
goto_distance(min_distance_um)
fluidics.open(1, 2, 3, 6)
pause(1)
reset_force()
goto_distance(max_distance_um)
while trap2.current_force < force_threshold_pN:
goto_distance(min_distance_um)
reset_force()
goto_distance(max_distance_um)
fluidics.close(1, 2, 3, 6)
stage.move_to("buffer")
goto_distance(min_distance_um)
reset_force()
from bluelake import Trap, stage, fluidics, pause, power, timeline, reset_force, confocal
reset_force()
timeline.mark_begin("FD1")
while Distancebeads.latest_value < 25:
trap1.move_by(dx=3, speed=8)
confocal.start_scan() # start the active configuration
# wait for scan to finish
pause(1)
while confocal.is_scanning:
pause(1)
timeline.mark_end()
print("Done!")