def setscale(imp,
scaleX=1.0,
scaleY=1.0,
scaleZ=1.0,
unit="micron"):
# check if scaleZ has a valid value to call modify the scaling
if scaleZ is None:
scaleZ = 1.0
# create new Calibration object
newCal = Calibration()
# set the new paramters
newCal.pixelWidth = scaleX
newCal.pixelHeight = scaleY
newCal.pixelDepth = scaleZ
# set the correct unit fro the scaling
newCal.setXUnit(unit)
newCal.setYUnit(unit)
newCal.setZUnit(unit)
# apply the new calibration
imp.setCalibration(newCal)
return imp
def prepare_image_stacks(image_dir):
""" For each stack directory in image_dir, load the image sequence as
a stack and spatially calibrate the stack.
Returns:
images (list): The list containing the calibrated image stacks.
Args:
image_dir (str): The directory containing the image stack directories.
"""
images = []
for stack_dir in os.listdir(image_dir):
stack_dir_full_path = str(image_dir) + '/' + stack_dir
imp = FolderOpener.open(stack_dir_full_path)
cal = Calibration()
cal.setUnit('um')
cal.pixelWidth = 0.3296485
cal.pixelHeight = 0.3296485
cal.pixelDepth = 0.998834955
imp.setCalibration(cal)
imp.setTitle(
stack_dir) # name the image after its directory, e.g. OP_1
images.append(imp)
return images
def setproperties(imp,
scaleX=1.0,
scaleY=1.0,
scaleZ=1.0,
unit="micron",
sizeC=1,
sizeZ=1,
sizeT=1):
"""Set properties of image in Fiji
:param imp: Image
:type imp: ImgPlus
:param scaleX: scaleX, defaults to 1.0
:type scaleX: float, optional
:param scaleY: scaleY, defaults to 1.0
:type scaleY: float, optional
:param scaleZ: scaleZ, defaults to 1.0
:type scaleZ: float, optional
:param unit: scale unit, defaults to "micron"
:type unit: str, optional
:param sizeC: sizeC, defaults to 1
:type sizeC: int, optional
:param sizeZ: sizeZ, defaults to 1
:type sizeZ: int, optional
:param sizeT: sizeT, defaults to 1
:type sizeT: int, optional
:return: Image
:rtype: ImgPlus
"""
# check if scaleZ has a valid value to call modify the properties
if scaleZ is None:
scaleZ = 1
# run the image properties tool
IJ.run(imp, "Properties...", "channels=" + str(sizeC) +
" slices=" + str(sizeZ)
+ " frames=" + str(sizeT)
+ " unit=" + unit
+ " pixel_width=" + str(scaleX)
+ " pixel_height=" + str(scaleY)
+ " voxel_depth=" + str(scaleZ))
# create new Calibration object
newCal = Calibration()
# set the new paramters
newCal.pixelWidth = scaleX
newCal.pixelHeight = scaleY
newCal.pixelDepth = scaleZ
# set the correct unit fro the scaling
newCal.setXUnit(unit)
newCal.setYUnit(unit)
newCal.setZUnit(unit)
# apply the new calibration
imp.setCalibration(newCal)
return imp
def set_xyz_calibration(imp, dx, dy, dz, unit): cal = Calibration(imp) cal.setUnit(unit) cal.pixelWidth = dx cal.pixelHeight = dy cal.pixelDepth = dz imp.setCalibration(cal) return imp
def setSpatialCalibration(img, xwidth, unit="micron"):
""" img is an image object from openImage()
xwidth is the width of the image in units (default micron)
"""
if xwidth <= 0:
# If spatial calibration is not given. Do not try to set it.
return
pixelSize = xwidth / (1.0*img.getWidth())
cal = Calibration(img)
cal.pixelWidth = pixelSize
cal.pixelHeight = pixelSize
cal.setUnit(unit)
img.setCalibration(cal)
return img
def setscale(imp,
scaleX=1.0,
scaleY=1.0,
scaleZ=1.0,
unit="micron"):
"""Set new scaling for image.
:param imp: image
:type imp: ImgPlus
:param scaleX: scaleX, defaults to 1.0
:type scaleX: float, optional
:param scaleY: scaleY, defaults to 1.0
:type scaleY: float, optional
:param scaleZ: scaleZ, defaults to 1.0
:type scaleZ: float, optional
:param unit: scaling unit, defaults to "micron"
:type unit: str, optional
:return: image
:rtype: ImgPlus
"""
# check if scaleZ has a valid value to call modify the scaling
if scaleZ is None:
scaleZ = 1.0
# create new Calibration object
newCal = Calibration()
# set the new paramters
newCal.pixelWidth = scaleX
newCal.pixelHeight = scaleY
newCal.pixelDepth = scaleZ
# set the correct unit fro the scaling
newCal.setXUnit(unit)
newCal.setYUnit(unit)
newCal.setZUnit(unit)
# apply the new calibratiion
imp.setCalibration(newCal)
return imp
def setproperties(imp,
scaleX=1.0,
scaleY=1.0,
scaleZ=1.0,
unit="micron",
sizeC=1,
sizeZ=1,
sizeT=1):
# check if scaleZ has a valid value to call modify the properties
if scaleZ is None:
scaleZ = 1
# run the image properties tool
IJ.run(imp, "Properties...", "channels=" + str(sizeC)
+ " slices=" + str(sizeZ)
+ " frames=" + str(sizeT)
+ " unit=" + unit
+ " pixel_width=" + str(scaleX)
+ " pixel_height=" + str(scaleY)
+ " voxel_depth=" + str(scaleZ))
# create new Calibration object
newCal = Calibration()
# set the new paramters
newCal.pixelWidth = scaleX
newCal.pixelHeight = scaleY
newCal.pixelDepth = scaleZ
# set the correct unit fro the scaling
newCal.setXUnit(unit)
newCal.setYUnit(unit)
newCal.setZUnit(unit)
# apply the new calibration
imp.setCalibration(newCal)
return imp
# Get image and calibrate
imps = BF.openImagePlus(input_file)
imp = imps[0]
imp.setDisplayMode(IJ.COLOR)
imp.setC(color)
# imp.setDisplayRange(0.0, 3.0)
# imp.show()
log_info += 'frames: ' + str(imp.getNFrames()) + '\n'
log_info += 'width: ' + str(imp.getWidth()) + '\n'
log_info += 'height: ' + str(imp.getHeight()) + '\n'
cal = Calibration()
cal.setUnit('micron')
cal.pixelHeight = resolution
cal.pixelWidth = resolution
cal.pixelDepth = 0.
cal.fps = 1
cal.frameInterval = 1
imp.setCalibration(cal)
#-------------------------
# Instantiate model object
#-------------------------
model = Model()
model.setPhysicalUnits('micron', 'frames')
# Set logger
model.setLogger(Logger.IJ_LOGGER)
def set_calibration_obj(metadata_dict):
cal = Calibration()
cal.setUnit(metadata_dict["unit"])
cal.pixelWidth = 1 / metadata_dict["xpix"]
cal.pixelHeight = 1 / metadata_dict["ypix"]
return cal
# osx, unix
filesep = '/'
home_dir = '/broad/blainey_lab/David/lasagna/20150817 6 round/data/'
home_dir = '/Users/feldman/Downloads/20151209/'
else:
# windows
home_dir = 'D:\\User Folders\\David\\lasagna\\20151122_96W-G020\\'
# home_dir = '\\\\neon-cifs\\blainey_lab\\David\\lasagna\\20150817 6 round\\analysis\\calibrated\\raw\\'
filesep = '\\'
data_dirs = ['stack']
cal = Calibration()
cal.setUnit('um')
cal.pixelWidth = pixel_width
cal.pixelHeight = pixel_width
def savename(well, data_dir):
# TODO better naming convention, use Site_0?
return home_dir + data_dir + '_MMStack_' + well + '.stitched.tif'
def stitch_cmd_file(directory, layout_file):
s = """type=[Positions from file] order=[Defined by TileConfiguration] directory=%s layout_file=%s fusion_method=[Linear Blending] regression_threshold=0.30 max/avg_displacement_threshold=2.50 absolute_displacement_threshold=3.50 computation_parameters=[Save computation time (but use more RAM)] image_output=[Fuse and display]"""
return s % (directory, layout_file)
for data_dir in data_dirs:
print home_dir + data_dir + filesep + '*.registered.tif'
files = glob(home_dir + data_dir + filesep + '*.registered.txt')
files = [f.split(filesep)[-1] for f in files]
# Set dimensions
n_channels = 1
n_slices = 1 # Z slices
n_frames = 1 # time frames
# Get current image
image = IJ.getImage()
# Check that we have correct dimensions
stack_size = image.getImageStackSize() # raw number of images in the stack
if n_channels * n_slices * n_frames == stack_size:
image.setDimensions(n_channels, n_slices, n_frames)
else:
IJ.log('The product of channels ('+str(n_channels)+'), slices ('+str(n_slices)+')')
IJ.log('and frames ('+str(n_frames)+') must equal the stack size ('+str(stack_size)+').')
# Set calibration
pixel_width = 1
pixel_height = 1
pixel_depth = 1
space_unit = 'µm'
frame_interval = 1
time_unit = 's'
calibration = Calibration() # new empty calibration
calibration.pixelWidth = pixel_width
calibration.pixelHeight = pixel_height
calibration.pixelDepth = pixel_depth
calibration.frameInterval = frame_interval
calibration.setUnit(space_unit)
calibration.setTimeUnit(time_unit)
image.setCalibration(calibration)
image.repaintWindow()
def process(srcDir, dstDir, currentDir, fileName, keepDirectories):
print "Processing:"
# Opening the image
print "Open image file", fileName
imp = IJ.openImage(os.path.join(currentDir, fileName))
#Here we make sure the calibration are correct
units = "pixel"
TimeUnit = "unit"
newCal = Calibration()
newCal.pixelWidth = 1
newCal.pixelHeight = 1
newCal.frameInterval = 1
newCal.setXUnit(units)
newCal.setYUnit(units)
newCal.setTimeUnit(TimeUnit)
imp.setCalibration(newCal)
cal = imp.getCalibration()
dims = imp.getDimensions() # default order: XYCZT
if (dims[4] == 1):
imp.setDimensions(1, 1, dims[3])
# Start the tracking
model = Model()
#Read the image calibration
model.setPhysicalUnits(cal.getUnit(), cal.getTimeUnit())
# Send all messages to ImageJ log window.
model.setLogger(Logger.IJ_LOGGER)
settings = Settings()
settings.setFrom(imp)
# Configure detector - We use the Strings for the keys
# Configure detector - We use the Strings for the keys
settings.detectorFactory = DownsampleLogDetectorFactory()
settings.detectorSettings = {
DetectorKeys.KEY_RADIUS: 2.,
DetectorKeys.KEY_DOWNSAMPLE_FACTOR: 2,
DetectorKeys.KEY_THRESHOLD: 1.,
}
print(settings.detectorSettings)
# Configure spot filters - Classical filter on quality
filter1 = FeatureFilter('QUALITY', 0, True)
settings.addSpotFilter(filter1)
# Configure tracker - We want to allow merges and fusions
settings.trackerFactory = SparseLAPTrackerFactory()
settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap(
) # almost good enough
settings.trackerSettings['LINKING_MAX_DISTANCE'] = LINKING_MAX_DISTANCE
settings.trackerSettings['ALLOW_TRACK_SPLITTING'] = ALLOW_TRACK_SPLITTING
settings.trackerSettings['SPLITTING_MAX_DISTANCE'] = SPLITTING_MAX_DISTANCE
settings.trackerSettings['ALLOW_TRACK_MERGING'] = ALLOW_TRACK_MERGING
settings.trackerSettings['MERGING_MAX_DISTANCE'] = MERGING_MAX_DISTANCE
settings.trackerSettings[
'GAP_CLOSING_MAX_DISTANCE'] = GAP_CLOSING_MAX_DISTANCE
settings.trackerSettings['MAX_FRAME_GAP'] = MAX_FRAME_GAP
# Configure track analyzers - Later on we want to filter out tracks
# based on their displacement, so we need to state that we want
# track displacement to be calculated. By default, out of the GUI,
# not features are calculated.
# The displacement feature is provided by the TrackDurationAnalyzer.
settings.addTrackAnalyzer(TrackDurationAnalyzer())
settings.addTrackAnalyzer(TrackSpeedStatisticsAnalyzer())
filter2 = FeatureFilter('TRACK_DISPLACEMENT', 10, True)
settings.addTrackFilter(filter2)
#-------------------
# Instantiate plugin
#-------------------
trackmate = TrackMate(model, settings)
#--------
# Process
#--------
ok = trackmate.checkInput()
if not ok:
sys.exit(str(trackmate.getErrorMessage()))
ok = trackmate.process()
if not ok:
sys.exit(str(trackmate.getErrorMessage()))
#----------------
# Display results
#----------------
if showtracks:
model.getLogger().log('Found ' +
str(model.getTrackModel().nTracks(True)) +
' tracks.')
selectionModel = SelectionModel(model)
displayer = HyperStackDisplayer(model, selectionModel, imp)
displayer.render()
displayer.refresh()
# The feature model, that stores edge and track features.
fm = model.getFeatureModel()
with open(dstDir + fileName + 'tracks_properties.csv', "w") as file:
writer1 = csv.writer(file)
writer1.writerow([
"track #", "TRACK_MEAN_SPEED (micrometer.secs)",
"TRACK_MAX_SPEED (micrometer.secs)", "NUMBER_SPLITS",
"TRACK_DURATION (secs)", "TRACK_DISPLACEMENT (micrometer)"
])
with open(dstDir + fileName + 'spots_properties.csv',
"w") as trackfile:
writer2 = csv.writer(trackfile)
#writer2.writerow(["spot ID","POSITION_X","POSITION_Y","Track ID", "FRAME"])
writer2.writerow(
["Tracking ID", "Timepoint", "Time (secs)", "X pos", "Y pos"])
for id in model.getTrackModel().trackIDs(True):
# Fetch the track feature from the feature model.
v = (fm.getTrackFeature(id, 'TRACK_MEAN_SPEED') *
Pixel_calibration) / Time_interval
ms = (fm.getTrackFeature(id, 'TRACK_MAX_SPEED') *
Pixel_calibration) / Time_interval
s = fm.getTrackFeature(id, 'NUMBER_SPLITS')
d = fm.getTrackFeature(id, 'TRACK_DURATION') * Time_interval
e = fm.getTrackFeature(
id, 'TRACK_DISPLACEMENT') * Pixel_calibration
model.getLogger().log('')
model.getLogger().log('Track ' + str(id) +
': mean velocity = ' + str(v) + ' ' +
model.getSpaceUnits() + '/' +
model.getTimeUnits())
track = model.getTrackModel().trackSpots(id)
writer1.writerow(
[str(id), str(v),
str(ms), str(s),
str(d), str(e)])
for spot in track:
sid = spot.ID()
x = spot.getFeature('POSITION_X')
y = spot.getFeature('POSITION_Y')
z = spot.getFeature('TRACK_ID')
t = spot.getFeature('FRAME')
time = int(t) * int(Time_interval)
writer2.writerow(
[str(id), str(t),
str(time), str(x),
str(y)])
def make_calibration(magnification):
cal = Calibration()
cal.setUnit('um')
cal.pixelWidth = args.magnification
cal.pixelHeight = cal.pixelWidth
return cal
def setCalibration(self, imp):
calibration = Calibration()
calibration.pixelWidth = self.pixelWidth
calibration.pixelHeight = self.pixelHeight
imp.setCalibration(calibration)
def setCalibration(self, imp): calibration=Calibration() calibration.pixelWidth=self.pixelWidth calibration.pixelHeight=self.pixelHeight imp.setCalibration(calibration)
template = None #or make_template('B1', '10X_c2-SBS-2_2')
data_dirs = ['test']
# usually xyzct, except on bad days when it's xyczt(default)
# order = 'xyzct'
order = 'xyczt(default)'
rows = 'ABH'
columns = [str(x) for x in range(1, 13)]
wells = [row + column for row in rows for column in columns]
wells = ['A1']
cal = Calibration()
cal.setUnit('um')
cal.pixelWidth = pixel_width
cal.pixelHeight = pixel_width
def savename(well, data_dir):
# TODO better naming convention, use Site_0?
return home_dir + data_dir + '_MMStack_' + well + '.stitched.tif'
def tile_config_name(well, data_dir):
return
def macro_dir(s):
"""Wrap directory string so ImageJ macro accepts it as parameter.
"""
return '[%s]' % (s.replace('\\', '\\\\'))
def setScale(self, distCm, distPixel):
cal = Calibration()
cal.setUnit("cm")
cal.pixelWidth = distCm / distPixel
cal.pixelHeight = distCm / distPixel
ImagePlus().setGlobalCalibration(cal)
n_channels = 1
n_slices = 1 # Z slices
n_frames = 1 # time frames
# Get current image
image = IJ.getImage()
# Check that we have correct dimensions
stack_size = image.getImageStackSize() # raw number of images in the stack
if n_channels * n_slices * n_frames == stack_size:
image.setDimensions(n_channels, n_slices, n_frames)
else:
IJ.log('The product of channels (' + str(n_channels) + '), slices (' +
str(n_slices) + ')')
IJ.log('and frames (' + str(n_frames) + ') must equal the stack size (' +
str(stack_size) + ').')
# Set calibration
pixel_width = 1
pixel_height = 1
pixel_depth = 1
space_unit = 'µm'
frame_interval = 1
time_unit = 's'
calibration = Calibration() # new empty calibration
calibration.pixelWidth = pixel_width
calibration.pixelHeight = pixel_height
calibration.pixelDepth = pixel_depth
calibration.frameInterval = frame_interval
calibration.setUnit(space_unit)
calibration.setTimeUnit(time_unit)
image.setCalibration(calibration)
image.repaintWindow()
filters.setup("median", frame)
filters.rank(processor, filter_window, filters.MEDIAN)
# Perform gamma correction
processor.gamma(gamma)
frame = ImagePlus("Frame " + str(frame_i), processor)
# Rolling ball background subtraction
processor = frame.getProcessor()
bg_subtractor = BackgroundSubtracter()
bg_subtractor.setup("", frame)
bg_subtractor.rollingBallBackground(processor, rolling_ball_size/pixel_size, False, False, False, False, True)
frame = ImagePlus("Frame " + str(frame_i), processor)
# Calibrate pixels
calibration = Calibration()
calibration.setUnit("pixel")
calibration.pixelWidth = pixel_size
calibration.pixelHeight = pixel_size
calibration.pixelDepth = 1.0
frame.setCalibration(calibration)
# Save to output dir
file_name = output_dir + "/" + str(frame_i).zfill(4) + ".tif"
FileSaver(frame).saveAsTiff(file_name)
frame_i = frame_i + 1
