def timeprogression(time, numsteps):
stepsize = round(time / numsteps, 2)
for i in range(1, numsteps + 1):
pause(stepsize)
print(" " + str(round(i * stepsize * 100 / time)) +
"% of time has elapsed (" + str(round(i * stepsize / 60, 1)) +
" min)")
def autoshutoffkymo(): #both force and photon counts
greenphoton = timeline["Photon count"]["Green"]
confocal.start_scan("RPA Kymo")
f1=trap2.current_force
print("initial force: " + str(round(f1,2)))
n=0; photonbin=20
while 1:
pause(1/78125)
n+=1
photonbin += greenphoton.latest_value
if n%(3000) == 0:
f2 = trap2.current_force
print("periodic check #"+str(round(n/3000)))
print(" photon count: " + str(photonbin))
print(" force: " + str(round(f2,2)))
if (photonbin < greencutoff) or (f2 < 0.5*f1):
pause(7)
break
else:
photonbin=0
confocal.abort_scan()
excitation_lasers.green = 0
print("!!!!!!!!! IT'S DONE !!!!!!!!!")
def pingpong(distance_delta_um, period_ms, speed):
while True:
trap1.move_by(dx=+distance_delta_um, speed=speed)
pause(period_ms / 1000 / 2)
log("ping")
trap1.move_by(dx=-distance_delta_um, speed=speed)
pause(period_ms / 1000 / 2)
log("pong")
def pressurecycle():
while fluidics.pressure < .6:
fluidics.increase_pressure()
pause(pt) #important!
while fluidics.pressure > 0.22:
fluidics.decrease_pressure()
pause(pt) #important!
print("pressure cycled")
def setpressure(pres):
curpres = fluidics.pressure
if curpres < pres:
while fluidics.pressure < pres:
fluidics.increase_pressure()
pause(0.1) #important!
else:
while fluidics.pressure > pres:
fluidics.decrease_pressure()
pause(0.1) #important!
def pingpong(distance_delta_um, period_ms, speed):
"""This will pingpong infinitely and must be stopped using the `Stop` button in the UI"""
while True:
trap1.move_by(dx=+distance_delta_um, speed=speed)
pause(period_ms / 1000 /
2) # pause time is given in seconds, convert from milliseconds
print("ping")
# reset_force() # optionally reset the force
trap1.move_by(dx=-distance_delta_um, speed=speed)
pause(period_ms / 1000 / 2)
print("pong")
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 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 stretchitout(stretchtime):
print("pre stretch time: "+ str(stretchtime) + " sec")
f1=trap2.current_force
print(" initial force: " + str(round(f1,2)))
trap = Trap("1", "XY")
trap.move_to(waypoint="more streatch",speed=4)
pause(stretchtime)
trap.move_to(waypoint="measure point",speed=4)
pause(2)
f2=trap2.current_force
print(" final force: " + str(round(f2,2)))
if f2<(0.5*f1) and f1 > 1:
print("it broke")
return 0
return 1
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 catch_beads(min_score=30):
target_traps = traps[:2]
# option 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)
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 goto_distance(target_distance, move_speed=8, force_limit=10000):
trap1, trap2 = traps[:2]
distance = timeline["Distance"]["Distance 1"]
dx = distance.latest_value - target_distance
while abs(dx) > 0.2:
if trap2.current_force > force_limit:
break
if dx <= 0:
trap1.move_by(dx=+abs(dx) * 0.8,
speed=move_speed) # MAYBE play around with this
else:
trap1.move_by(dx=-abs(dx) * 0.8, speed=move_speed)
dx = distance.latest_value - target_distance
# print(dx)
# print("till here")
pause(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
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 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 ssDNAstretch(): #0 if nothing/broke, 1 if good, 2 if unsuccessful pull
success = 0
trap.move_to(waypoint="stretched", speed=6)
trap.move_by(dx=12, speed=1)
pause(0.5)
highforce = trap2.current_force
trap.move_by(dx=-12, speed=1)
lowforce = trap2.current_force
print(" -ssDNA: " + str(round(lowforce, 2)) + " to " +
str(round(highforce, 2)))
if highforce > 50:
print(" extension ok")
success = 1
if lowforce > 20:
print(" looks like its still dsDNA")
success = 2
if success == 0:
print(" ssDNA broke ;-;")
fluidics.open(1, 2, 3, 6)
if success == 1:
print(" ssDNA done !!!!")
return success
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cNo..lKKKKKKKKKl.....'dKKKKKxc,l0:
.c:'.lKKKKKKKKKk;....lKKKKKKo'.oNc
,:.'oxOKKKKKKKOxxxxOKKKKKKxc,;ol:.
;c..'':oookKKKKKKKKKKKKKKKKKk:.'clc.
,xl'.,oxo;'';oxOKKKKKKKKKKKKKKKOxxl:::;,.
.dOc..lKKKkoooookKKKKKKKKKKKKKKKKKKKxl,;ol.
cx,';okKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKl..;lc.
co..:dddddddddddddddddddddddddddddddddl::',::.
co........................................... """
print(parrot)
#%% MAIN ========================================
excitation_lasers.green = 0
goodstretch = stretchitout(25)
#goodstretch=1
if goodstretch:
f1=trap2.current_force
gogetprotein(10,1,f1) #sec to hang out, 1=flow on, initial force
pause(1)
f2 = trap2.current_force
if f2 > 0.5*f1 or f1 < 2:
excitation_lasers.green=40
pause(2)
autoshutoffkymo()
parrot()
else:
print("something is wrong!!")
from bluelake import fluidics, pause
# Open specific valves
fluidics.open(1, 2, 3, 6)
# or
fluidics.open(1, 2)
# And close valves
fluidics.close(1, 2)
# Read the current pressure value
print(fluidics.pressure)
# Pressure control does the same thing as the UI (not really ideal)
fluidics.increase_pressure()
fluidics.decrease_pressure()
while fluidics.pressure < 1: # bar
fluidics.increase_pressure()
pause(1) # seconds to pause -- important because pressure changes are slow
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!")
reset_force()
print("initialized position")
#initialize variables
pforce_old = pingpongforce()
pforce = pforce_old
caught = 0
attempts = 1
print("initialized variables (old=" + str(round(pforce_old, 2)) + ")")
#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")
pforce = pingpongforce()
print(" new force =" + str(round(pforce, 2)))
if (pforce_old * 0.77) > pforce or pforce > (pforce_old * 1.23):
caught = 1
else:
pforce_old = pforce
if (attempts % 15) == 0:
pressurecycle()
attempts += 1
print("hopefully we finished")
#hopefully caught something, move to buffer channel and reset all
stage.move_to("buffer")
"""Automated bead catching of 1 bead"""
from bluelake import stage, fluidics, pause, trap1, timeline
match_score = timeline["Tracking Match Score"]["Bead 1"]
trap1.clear() # to get rid of any existing bead
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 match_score.latest_value < match_threshold:
# We only want to clear the trap if there's a bead there, so > 0% match
if 0 < match_score.latest_value < match_threshold:
print("Rejected bead with match score:", match_score.latest_value)
trap1.clear() # bad bead, BAD bead
pause(0.5) # seconds
stage.move_to("buffer")
fluidics.close(1, 2, 3, 6)
def wait_for_scan():
"""Wait for the last confocal scan to finish"""
pause(1)
while confocal.is_scanning:
pause(1)
reset_force()
print("initialized position")
#initialize variables
pforce_old=pingpongforce()
pforce=pforce_old
caught=0
attempts=1
print("initialized variables ("+str(round(pforce_old,2)))
#moving into dna channel and starting pingpong
while caught!=1:
print(" we've attempted "+str(attempts)+" times")
print(" old force ="+str(round(pforce_old,2)))
stage.move_to("DNA")
pause(0.5)
stage.move_to("buffer")
pforce=pingpongforce()
#print(" new force ="+str(round(pforce)))
if (pforce_old*0.8)>pforce or pforce>(pforce_old*1.2):
caught=1
else:
pforce_old=pforce
attempts+=1
if (attempts%15)==0:
pressurecycle()
print("hopefully we finished")
#hopefully caught something, move to buffer channel and reset all
stage.move_to("buffer")
"""Smooth high-frequency trap oscillation See docs at https://help.lumicks.com/bluelake-api/api.html#bluelake.Trap.start_oscillation """ from bluelake import trap1, pause # Start a 10 Hz oscillation, with amplitude 1 um trap1.start_oscillation(axis="x", frequency=10, amplitude=1) # Let it run for 5 seconds, then stop pause(5.0) trap1.stop()
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!")
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")
print('start executing script')
# set up the pressure
while fluidics.pressure < .20:
fluidics.increase_pressure()
pause(1) #important!
pause(5)
single_tether_count = 0
mult_tether_count = 0
number_of_tries = 0
# this is going to be a for loop that can be broken
for jj in range(10):
# while single_tether_count < 100:
start = time.time()
number_of_tries += 1
bead_DNA_complex_setup()
end = time.time()
