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 !!!!!!!!!")
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!")
# 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")
print("Scan started: " + str(imagetime) + "sec")
timeprogression(imagetime, 10)
# stop imaging
confocal.abort_scan()
#turn off laser
excitation_lasers.green = 0
print("!!!! Scan ended !!!!")
from bluelake import confocal, excitation_lasers, pause
print(excitation_lasers.red) # get current value in %
excitation_lasers.red = 40 # set value in %
confocal.start_scan() # start the active configuration
confocal.start_scan("Preset name") # start a specific preset
# wait for scan to finish (not required)
pause(1)
while confocal.is_scanning:
pause(1)
# or abort scan
confocal.abort_scan()
def increment_frap_count():
"""Add or increment a FRAP counter for the timeline markers"""
if not hasattr(bluelake, "frap_count"):
bluelake.frap_count = 0
bluelake.frap_count += 1
increment_frap_count()
timeline.mark_begin(f"FRAP {bluelake.frap_count}")
# Scan 1: Before using this script you must save a scan preset and name it
# "reference" (or anything else that matches the `start_scan()` below).
excitation_lasers.blue = 15 # % power
# and/or: `excitation_lasers.red = 20` # % power
confocal.start_scan("reference")
wait_for_scan()
# Scan 2: As above, this starts a scan preset called "bleach". You must save
# this preset in the UI before starting the script.
excitation_lasers.blue = 90 # % power
confocal.start_scan("bleach")
wait_for_scan()
# Scan 3: The previous two were single-frame scans, but this one is usually
# multi-frame (again, set this in the UI and save it). It can also
# be useful to increase the "Image time" in the UI. Effectively,
# this adds a pause between frames in order to avoid bleaching if
# the recovery is slow.
excitation_lasers.blue = 15 # % power
confocal.start_scan("image")
from bluelake import pause, confocal
iterations = 20
preset_name = "single_kymo"
for i in range(iterations):
confocal.start_scan(preset_name)
pause(1)
# MAIN ======================================
hangtime = 5 #how long it stays stretched
imagetime = 500 #how long to image for
proteintime = 5 #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 = 20
#start imaging
confocal.start_scan("SSB kymo")
print("Scan started: " + str(imagetime) + "sec")
timeprogression(imagetime, 10)
# stop imaging
confocal.abort_scan()
#turn off laser
excitation_lasers.green = 0
print("!!!! Scan ended !!!!")