def OnNewPoint(x, y, z, position):
global rs
global count
global output
global action
global current_cube_index
global aborted
if aborted:
pass
output_directory = output[0]
filename = output[1]
filename_ext = output[2]
subdir = '%s\\Cube%d\\Region%d\\' % (output_directory,
cubes[current_cube_index], count)
try:
os.makedirs(subdir)
except (OSError):
print 'os.makedirs(' + subdir + ') FAILED'
print z
print focus_offsets[current_cube_index]
microscope.SetStagePosition(x, y, z + focus_offsets[current_cube_index])
# Wait for stage to finish moving (additional delay=0.1 seconds, time out = 1.0 seconds)
microscope.WaitForStage(0.0, 5.0)
rs.SetRelativeRoi(x_size, y_size)
rs.Start(action, subdir, filename, filename_ext)
count = count + 1
def OnNewPoint(x, y, z, position):
global current_cube_index
global aborted
z_centre = z + focus_offsets[current_cube_index]
dir = output[0] + 'Point' + str(position)
if not os.path.exists(dir):
os.mkdir(dir)
for z_current_step in range(-z_images_below, z_images_above +
1): # +1 ensures the last point is aquired
if aborted:
break
z_current = z_centre + z_step * z_current_step
print "Capturing image at (z = ", str(z_current), ")"
microscope.SetStagePosition(x, y, z_current)
microscope.WaitForStage(0.0, 1.0)
filename = microscope.ParseSequenceFilename(output[1], position)
zpos = '%(#)02d' % {"#": (z_current_step + z_images_below)}
filename = microscope.InsertTextIntoFilename(filename, "z" + zpos)
filename = microscope.InsertCubeIntoFilename(filename,
cubes[current_cube_index])
path = dir + os.sep + filename
microscope.SnapAndSaveImage(path)
def Move(x, y, z, cube_index):
print "Moving to (%d,%d)" % (x, y)
# Apply focus offset
microscope.SetStagePosition(x, y, z + focus_offsets[cube_index])
# Wait for stage to finish moving (additional delay=0.1 seconds, time out = 1.0 seconds)
microscope.WaitForStage(0.0, 5.0)
def OnNewPoint(x, y, z, position):
microscope.SetStagePosition(x, y, z)
# Wait for stage to finish moving (additional delay=0.1 seconds, time out = 1.0 seconds)
microscope.WaitForStage(0.0, 1.0)
microscope.SnapImage()
def OnNewPoint(x, y, z, position):
microscope.SetStagePosition(x, y, z)
# 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
microscope.SnapAndSaveImage(path)
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 current_cube_index
microscope.SetStagePosition(x, y, z + focus_offsets[current_cube_index])
# 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
microscope.SnapAndSaveImage(path)
def OnNewPoint(x, y, z, position):
# print "Moving Stage ", (x, y, z)
microscope.SetStagePosition(x, y, z)
#print "Moved Stage to ", microscope.MicroscopeGetStagePosition()
# wait for stage to finish moving (additional delay=0.1 seconds, time out = 1.0 seconds)
microscope.WaitForStage(0.0, 1.0)
#print "Snapping Image"
microscope.SnapImage()
def OnNewPoint(x, y, z, position):
global aborted, point_list
print "Point: ", position
print("input: x %f, y %f, z %f" % (x, y, z))
print "list: ", point_list[position - 1][2]
# Adjust z to last autofocus position, first time round these two will be the same
z = point_list[position - 1][2]
print "Adjust z to last autofocus position: z=", z
if aborted:
pass
microscope.SetStagePosition(x, y, z)
# 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_ext = output[2]
#filename = microscope.ParseSequenceFilename(filename, position)
#filename = microscope.InsertCubeIntoFilename(filename, current_cube_index+1)
#subdir = '%s\\Cube%d\\Region%d\\' % (output_directory, cubes[current_cube_index], position)
#subdir = '%s\\Region%d\\' % (output_directory, position)
subdir = '%s\\Region%d_%s\\' % (output_directory, position,
time.strftime("%d%b%Y_%Hh%Mm%Ss",
time.localtime(time.time())))
try:
os.makedirs(subdir)
except (OSError):
print 'os.makedirs(' + subdir + ') FAILED'
print "Autofocus"
microscope.PerformSoftwareAutoFocus()
autoFocusedZPosition = microscope.GetStagePosition()[2]
point_list[position - 1][2] = autoFocusedZPosition
print "Auto focused position stored:", point_list[position - 1][2]
# get the focal plane options for this region and transfer to the region scan module, correct for the autofocus
rs.SetFocalPlaneOptions(microscope.GetFocalPlaneOptions())
rs.SetFocalPlaneOffsetFromXYZ(x, y, autoFocusedZPosition)
# Set region scan with the region width and height
rs.SetRelativeRoiFromTimelapse(microscope.GetTimeLapseRegion())
rs.Start(action, subdir, filename, filename_ext)
rs.Hide()
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 OnNewPoint(x, y, z, position):
global current_cube_index, camera_acq
microscope.SetStagePosition(x, y, z + focus_offsets[current_cube_index])
# 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
if camera_acq == 1:
print "Camera image: ", position
microscope.SnapAndSaveImage(path)
else:
print "Performing SPC: ", position
spc.ClearBoardMemory()
spc.AcquireAndSaveToFileUsingUIValues(1, path)
def OnNewPoint(x, y, z, position):
microscope.MoveOpticalPathToPosition(2)
microscope.MoveCubeToPosition(1)
microscope.WaitForCube(0.0, 10.0)
# print "Moving Stage ", (x, y, z)
microscope.SetStagePosition(x, y, z)
# 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 AutoFocus"
#microscope.PerformSoftwareAutoFocus(path)
#microscope.SnapAndSaveImage(path)
microscope.MoveOpticalPathToPosition(4)
microscope.MoveCubeToPosition(2)
microscope.WaitForCube(0.0, 10.0)
print "Performing SPC"
microscope.StartSPC(path)
def OnNewPoint(x, y, z, position):
# print "Moving Stage ", (x, y, z)
microscope.SetStagePosition(x, y, z)
# 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
microscope.PerformSoftwareAutoFocus(path)
microscope.SnapAndSaveImage(path)
#mrowley - 081209 - recording the software auto focus determined focal point for the given well
xf, yf, zf = microscope.GetStagePosition()
filenameautopts = 'AutoFocusedPlane.pts'
path = output[0] + filenameautopts
fileautopts = open(path, 'a')
fileautopts.write('%.2f' %xf + '\t' + '%.2f' %yf + '\t' + '%.2f' %zf + '\n')
fileautopts.close()
def OnNewPoint(x, y, z, position):
global core
global output
global cube_data
output_directory = output[0]
filename = output[1]
filename_ext = output[2]
# Move to first cube to perform autofocus.
microscope.MoveCubeToPosition(1)
# AutoFocus Once for each new point (centre point)
print "Performing AutoFocus"
microscope.PerformSoftwareAutoFocus()
for cube in cubes:
if aborted:
return;
print "Setting camera exposure to ", exposures[cube - 1]
microscope.SetExposure(exposures[cube - 1])
print "Setting camera gain to ", gains[cube - 1]
microscope.SetGain(gains[cube - 1])
cube_details = cube_data[cube - 1]
print "Moving to cube position ", cube
microscope.MoveCubeToPosition(cube)
print "Moving to (%d,%d)" % (x, y)
# Apply focus offset
microscope.SetStagePosition(x, y, z + focus_offsets[cube - 1])
# Wait for stage to finish moving (additional delay=0.1 seconds, time out = 1.0 seconds)
microscope.WaitForStage(0.0, 5.0)
filepath = '%s\\%s_Core%d_%s%s' % (output_directory, filename, core, cube_details["Name"], filename_ext)
print "Saving file: ", filepath
microscope.SnapAndSaveImage(filepath)
core = core + 1
def OnNewPoint(x, y, z, position):
global aborted, cube, offset
print "Point: ", position
if aborted:
pass
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 and save ", path
microscope.SnapAndSaveImage(path)
def OnNewPoint(x, y, z, position):
global aborted
print "Point: ", position
if aborted:
pass
microscope.SetStagePosition(x, y, z)
# 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_ext = output[2]
#filename = microscope.ParseSequenceFilename(filename, position)
#filename = microscope.InsertCubeIntoFilename(filename, current_cube_index+1)
#subdir = '%s\\Cube%d\\Region%d\\' % (output_directory, cubes[current_cube_index], position)
#subdir = '%s\\Region%d\\' % (output_directory, position)
subdir = '%s\\Region%d_%s\\' % (output_directory, position, time.strftime("%d%b%Y_%Hh%Mm%Ss", time.localtime(time.time())))
try:
os.makedirs(subdir)
except (OSError):
print 'os.makedirs(' + subdir + ') FAILED'
# get the focal plane options for this region and transfer to the region scan module
rs.SetFocalPlaneOptions(microscope.GetFocalPlaneOptions())
# Set region scan with the region width and height
rs.SetRelativeRoiFromTimelapse(microscope.GetTimeLapseRegion())
rs.Start(action, subdir, filename, filename_ext)
rs.Hide()
def OnNewPoint(x, y, z, position):
global aborted, cube_data
print "Point: ", position
if aborted:
pass
output_directory = output[0]
filename_ext = output[2]
subdir = '%sRegion%d\\' % (
output_directory, position
) # all cubes in one folder for Mosaic to make a composite RGB mosaic
#subdir = '%s\\Region%d_%s\\' % (output_directory, position, time.strftime("%d%b%Y_%Hh%Mm%Ss", time.localtime(time.time()))) # use this to time stamp each region mosaic
try:
os.makedirs(subdir)
except (OSError):
print 'os.makedirs(' + subdir + ') FAILED - folder may exist already.'
for cube in cube_data:
if aborted:
break
print "Moving to region centre (%d,%d)" % (x, y)
microscope.SetStagePosition(
x, y, z) # no need to apply z offset here, use it below
# Wait for stage to finish moving (additional delay seconds, time out seconds)
microscope.WaitForStage(0.0, 1.0)
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])
#filename = output[1]
#filename = microscope.InsertCubeIntoFilename(filename, cube['Position']) # do not use this here as filename from the simple select dialog does not have an extension, safer is the following
filename = output[1] + "_" + cube['Name']
print filename
# individual folders for cubes
#subdir = '%sCube%d\\Region%d\\' % (output_directory, cube['Position'], position)
#try:
# os.makedirs(subdir)
#except (OSError):
# print 'os.makedirs(' + subdir + ') FAILED'
# get the focal plane options for this region and transfer to the region scan module
print "Offset focal plane by ", options[2]
rs.SetFocalPlaneOptions(microscope.GetFocalPlaneOptions()
) # timelapse based focal plane/options
rs.SetFocalPlaneOffset(options[2]) # cube based offset
# Set region scan with the region width and height
print "Scanning Region"
rs.SetRelativeRoiFromTimelapse(microscope.GetTimeLapseRegion())
rs.Start(action, subdir, filename, filename_ext)
rs.Hide()