def OnNewPoint(x, y, z, position):
global aborted, spc
print "Point: ", position
if aborted:
break
print "Set Fluorescence Mode"
microscope.MicroscopeSetMode(0)
for cube in cube_data:
print "Selecting Cube ", cube['Position'], ": ", cube['Name']
microscope.MoveCubeToPosition(cube['Position'])
options = microscope.GetCubeOptions(
cube['Position']) # camera exposure, gain and focus offset
print "Setting camera exposure to ", options[0]
microscope.SetExposure(options[0])
print "Setting camera gain to ", options[1]
microscope.SetGain(options[1])
# store the focus offset
offset = options[2]
if aborted:
break
print "Moving to (%0.1f, %0.1f, %0.1f)" % (x, y, z + offset)
microscope.SetStagePosition(x, y, z + offset)
# Wait for stage to finish moving (additional delay seconds, time out seconds)
microscope.WaitForStage(0.0, 1.0)
output_directory = output[0]
filename = output[1]
filename = microscope.ParseSequenceFilename(filename, position)
filename = microscope.InsertCubeIntoFilename(filename,
cube['Position'])
path = output_directory + filename
print "Acquire with FL cube: ", path
microscope.SnapAndSaveImage(path)
if aborted:
pass
print "Set Laser Scanning Mode"
microscope.MicroscopeSetMode(2) # Laser Scanning
spc.ClearBoardMemory()
filename = microscope.ParseSequenceFilename(output[1], position)
filename = microscope.InsertTextIntoFilename(filename, "spc")
path = output[0] + filename
print "Acquire with SPC: ", path
spc.AcquireAndSaveToFileUsingUIValues(1, path)
def OnNewPoint(x, y, z, position):
global spc
microscope.SetStagePosition(x, y, z)
# microscope.SetStagePosition(x, y, (z+11.50))
# wait for stage to finish moving (additional delay=0.1 seconds, time out = 1.0 seconds)
microscope.WaitForStage(0.0, 1.0)
filename = microscope.ParseSequenceFilename(output[1], position)
path = output[0] + filename
print "Performing SPC"
microscope.MicroscopeSetMode(2) # Laser Scanning
spc.ClearBoardMemory()
spc.AcquireAndSaveToFileUsingUIValues(1, path)
microscope.MicroscopeSetMode(0) # FLuorescence
filename = microscope.ParseSequenceFilename(output[1], position)
path = output[0] + filename
microscope.SnapAndSaveImage(path)
def OnCycleStart():
global current_cube_index, camera_acq
current_cube_index = 0
print "Fluorescence Mode"
microscope.MicroscopeSetMode(0) # FLuorescence
camera_acq = 1 # do the widefield camera images now
for cube in cubes:
print "Moving to cube position ", cube
microscope.MoveCubeToPosition(cube)
print "Setting camera exposure to ", exposures[current_cube_index]
microscope.SetExposure(exposures[current_cube_index])
microscope.VisitPoints()
current_cube_index = current_cube_index + 1
print "Laser Scanning Mode"
camera_acq = 0 # do the flim images now
microscope.MicroscopeSetMode(2) # Laser Scanning
microscope.VisitPoints()
import microscope
import time
try:
print help(microscope.MicroscopeSetMode)
print "Setting microscope to mode FLUORESCENCE_MODE"
microscope.MicroscopeSetMode(FLUORESCENCE_MODE)
time.sleep(2)
print "Setting microscope to mode BRIGHT_FIELD_MODE"
microscope.MicroscopeSetMode(BRIGHT_FIELD_MODE)
except:
print "Could not change mode"