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 bead_DNA_complex_setup():
fluidics.open(1, 2, 3, 6)
fluidics.close(4, 5)
pause(5) # wait for flow to start
stage.move_to("beads")
print("Moved to Beads channel")
catch_beads(80)
print("Beads are trapped")
# stage.move_to("DNA")
# print("Moved to DNA channel")
# pause(5) ## DEFINITELY have to play with this based on DNA concentration/flow rate
# print('till here')
stage.move_to("buffer")
print("Moved to Buffer channel")
def catch_beads(min_score=30): #from Zsombor
stage.move_to("beads")
target_traps = traps[:2]
target_traps[1].clear()
target_traps[0].clear()
bead1 = timeline['Tracking Match Score']['Bead 1']
bead2 = timeline['Tracking Match Score']['Bead 2']
bead_scores = [bead1, bead2]
while any(bead.latest_value < min_score for bead in bead_scores):
if any(0 < bead.latest_value < min_score for bead in bead_scores):
for trap in target_traps:
trap.clear() # bad beads
print('bad beads')
pause(1)
print("beads should be caught")
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()
def catch_2_beads():
"Just like `abc2.py`"
target_traps = [trap1, trap2]
match_scores = [match_score1, match_score2]
for trap in target_traps:
trap.clear() # to get rid of any existing beads
stage.move_to("beads") # must match the label in the UI
fluidics.open(1, 2, 3, 6) # list of valves to open matching the UI
match_threshold = 80 # % minimal match score
while any(m.latest_value < match_threshold for m in match_scores):
if any(0 < m.latest_value < match_threshold for m in match_scores):
for trap in target_traps:
trap.clear() # bad beads
pause(1)
stage.move_to("buffer")
fluidics.close(1, 2, 3, 6)
def gogetprotein(hangouttime,flowon,initforce):
print("getting protein for " + str(hangouttime) + " sec")
trap = Trap("1", "XY")
trap.move_to(waypoint="measure point",speed=4)
stage.move_to("J1")
stage.move_to("Ch1")
setpressure(0.12)
if flowon:
fluidics.open(1,2,3,4,6)
pause(hangouttime)
fluidics.close(1,2,3,4,6)
stage.move_to("J1")
stage.move_to("buffer")
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 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
"""Automated bead catching -- 2 beads"""
from bluelake import stage, fluidics, pause, timeline, trap1, trap2
target_traps = [trap1, trap2]
match_score1 = timeline["Tracking Match Score"]["Bead 1"]
match_score2 = timeline["Tracking Match Score"]["Bead 2"]
match_scores = [match_score1, match_score2]
for trap in target_traps:
trap.clear() # to get rid of any existing beads
stage.move_to("beads") # must match the label in the UI
fluidics.open(1, 2, 3, 6) # list of valves to open matching the UI
# Note: `match_score1` does not map directly to `trap1`. `match_score1`,
# `match_score2` sort beads from left to right, up to down. In case we
# `match_score1.latest_value > 0` we can't be sure that if that bead is
# in `trap1` or `trap2`. So to catch 2 beads we need to make sure both
# are good or clear both traps even if just one is bad.
match_threshold = 80 # % minimal match score
while any(m.latest_value < match_threshold for m in match_scores):
if any(0 < m.latest_value < match_threshold for m in match_scores):
for trap in target_traps:
trap.clear() # bad beads
pause(1)
stage.move_to("buffer")
fluidics.close(1, 2, 3, 6)
trap = Trap("1", "XY")
pt = 0.1
spd = 35
#functions that may be helpful
def setpressure(pres):
curpres = fluidics.pressure
if curpres < pres:
while fluidics.pressure < pres:
fluidics.increase_pressure()
pause(pt) #important!
else:
while fluidics.pressure > pres:
fluidics.decrease_pressure()
pause(pt) #important!
# MAIN-----------------------------------------------------------
print("moving to ch1")
stage.move_to("J1", speed=spd)
stage.move_to("Ch1", speed=spd)
print("waiting...")
pause(10)
print("done waiting, time to move")
stage.move_to("J1", speed=spd)
stage.move_to("buffer", speed=spd)
print("done moving, start imaging!")
print("hopefully we finished")
return 1
#THIS IS THE START OF THE MAIN -----------------------------------------
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")
#if want to move to ch4 to ready for experiment start
if echannel == 1:
movetoch4()
trap.move_to(waypoint="Point 2", speed=3)
print('ready to image!')
if any(0 < bead.latest_value < min_score for bead in bead_scores):
for trap in target_traps:
trap.clear() # bad beads
print('bad beads')
pause(1)
print("beads should be caught")
#THIS IS THE START OF THE MAIN -----------------------------------------
#check for beads first
bt = beadtest()
if bt == 0:
setpressure(0.3)
fluidics.open(1, 2, 3, 6)
stage.move_to("beads")
catch_beads(82)
else:
#turn on fluidics
fluidics.open(1, 2, 3, 6)
# set up the pressure
stage.move_to("buffer")
setpressure(0.22)
#set traps at initial position and reset force
gohome()
reset_force()
print("initialized position")
#initialize variables