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 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 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)")
# MAIN ======================================
hangtime = 5 #how long it stays stretched
imagetime = 400 #how long to image for
proteintime = 3 #waiting for protein to bind
excitation_lasers.green = 0
trap = Trap("1", "XY")
# stretching
print("stretching for " + str(hangtime) + " sec")
trap.move_to(waypoint="more streatch", speed=5)
timeprogression(hangtime, 5)
trap.move_to(waypoint="measure point", speed=5)
print("stretch done")
print("just hanging out for a bit for protein binding (" + str(proteintime) +
" sec)")
timeprogression(proteintime, 5)
#turn on laser
excitation_lasers.green = 30
#start imaging
confocal.start_scan("Rep kymo")
#to move from imaging channel to buffer channel slowly
#assumptions:start from 'buffer' channel at least?
from bluelake import Trap, stage, fluidics, pause, reset_force
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")
#trapping dna with ping pong automation
#will catch your beads
from bluelake import Trap, stage, fluidics, pause, reset_force, timeline, traps
import numpy as np
trap = Trap("1", "XY")
trap2 = Trap("2", "XY")
pt = 0.1
echannel = 1 #change this to 1 if you want to end in an experiment channel
dnadwell = 1 #how long to dwell in dna channel (sec)
makessDNA = 1
#functions that we need to catch DNA
def pingpongforce():
trap.move_by(dx=10, speed=5.5)
ppf = trap.current_force
trap.move_by(dx=-10, speed=6.5)
return ppf
def pingpongforce2():
trap.move_by(dx=9, speed=5.5)
ppf1 = trap2.current_force
move_by2(1.2, 5.5)
ppf2 = trap2.current_force
trap.move_by(dx=-10.2, speed=6.5)
print(" " + str(round(ppf1, 2)) + " to " + str(round(ppf2, 2)))
if (ppf1 * 0.77) > ppf2 or ppf2 > (ppf1 * 1.23):
return 1
#import bluelake_remote
from bluelake import Trap, pause, log
trap1 = Trap("1", "XY")
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")
log("Running pingpong script")
pingpong(distance_delta_um=0.008, period_ms=50, speed=0)
# 1) move trap into 'measure point' position and hang out in the 'protein'
# 2) move back into the buffer channel
# 3) start image
# 4) record starting force and photon count
# 5) if force goes below cutoff, wait n time and stop scan
# if photon count goes below cutoff, wait n time and stop scan,
# then return to the protein channel
from bluelake import pause, timeline, confocal, Trap, stage, fluidics, excitation_lasers
import numpy as np
greencutoff = 11
#%% FUNCTIONS ====================
trap2 = Trap("2","XY")
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
#trapping dna with ping pong automation
#will catch your beads
from bluelake import Trap, stage, fluidics, pause, reset_force, timeline, traps
import numpy as np
trap = Trap("1", "XY")
pt = 0.1
echannel = 0 #change this to 1 if you want to end in an experiment channel
dnadwell = 1.5 #how long to dwell in dna channel (sec)
dist1pp = 1.6
# dist1pp = 10
#functions that we need to catch DNA
def pingpongforce():
trap.move_by(dx=(10 + dist1pp), speed=5.5)
ppf = trap.current_force
trap.move_by(dx=-(dist1pp + 10), speed=6.5)
return ppf
def pingpongforce2():
trap.move_by(dx=(9 + dist1pp), speed=5.5)
ppf1 = trap.current_force
move_by2(1.2, 5.5)
ppf2 = trap.current_force
trap.move_by(dx=-(10.2 + dist1pp), speed=6.5)
print(" " + str(round(ppf1, 2)) + " to " + str(round(ppf2, 2)))
if (ppf1 * 0.77) > ppf2 or ppf2 > (ppf1 * 1.23):
return 1