fileout = os.path.join(analyzeDir, os.path.basename(filepath))
IJ.saveAs(impOut, "Jpeg", fileout)
def createOutputImg(image, roim, centPart, metaphase):
#maximal projection
imp = image
if image.getNSlices() > 1:
zp = ZProjector()
zp.setMethod(zp.MAX_METHOD)
zp.setImage(image)
zp.doProjection()
imp = zp.getProjection()
else:
imp = image
IJ.run(imp,"Enhance Contrast", "saturated=0.35")
IJ.setForegroundColor(255,0,0)
#need to show the image to draw overlay
imp.show()
IJ.run(imp,"RGB Color", "");
for i in range(roim.getCount()):
roim.select(imp, i)
roim.runCommand("Draw")
if metaphase:
IJ.setForegroundColor(0,255,255)
else:
IJ.setForegroundColor(0,255,0)
roim.select(imp, centPart)
def getMIP(stackImp):
"""
Create a maximum intensity projection (MIP) from an ImagePlus stack
@return ImagePlus maximum projection
"""
zp = ZProjector(stackImp)
zp.setMethod(ZProjector.MAX_METHOD)
zp.setStopSlice(stackImp.getNSlices())
zp.doHyperStackProjection(False)
return zp.getProjection()
def projectionImage(imp):
"""Returns the MIP of the specified ImagePlus (a composite stack)"""
from ij.plugin import ZProjector
roi_exists = imp.getRoi() is not None
imp.deleteRoi()
zp = ZProjector(imp)
zp.setMethod(ZProjector.MAX_METHOD)
zp.setStartSlice(1)
zp.setStopSlice(imp.getNSlices())
zp.doHyperStackProjection(True)
mip_imp = zp.getProjection()
mip_imp.setCalibration(imp.getCalibration())
if roi_exists:
mip_imp.restoreRoi()
return mip_imp
def project_z(imp, method):
zp = ZProjector(imp)
if method=="max":
zp.setMethod(ZProjector.MAX_METHOD)
if method=="sum":
zp.setMethod(ZProjector.SUM_METHOD)
zp.setStopSlice(imp.getNSlices())
zp.doHyperStackProjection(True)
zpimp = zp.getProjection()
#IJ.run(imp, "Z Project...", "projection=[Max Intensity] all");
#impout = IJ.getImage()
return zpimp
def main():
#opens the image and gets its name
# imp = open_test_img()
# imp.show()
imp = IJ.getImage()
title = imp.getTitle()
basename, extension = splitext(title)
# does a minimum projection and makes a mask
imp_min = ZProjector.run(imp, 'min')
ip = imp_min.getProcessor()
ip.setThreshold(1, 9999999999, 1)
mask = ip.createMask()
mask = ImagePlus("mask", mask)
# fills in the holes in the mask
IJ.run(mask, "Invert", "")
IJ.run(mask, "Fill Holes", "")
IJ.run(mask, "Invert", "")
# converts to list and then finds the crop coordinates
px = mask.getProcessor().getPixels()
px = [-int(_) for _ in px] #for some reason the 1s are -1 here
px = reshape(px, (imp.height, imp.width))
crop_top_left, crop_width, crop_height = find_largest_rectangle_2D(px)
# crops the original image
imp.setRoi(crop_top_left[0], crop_top_left[1], crop_width, crop_height)
imp_cropped = imp.resize(crop_width, crop_height, "bilinear")
imp_cropped.setTitle(basename + "_autocrop" + extension)
imp_cropped.show()
def perform_cropping(imp, info, output_folder, default_path):
imp.show()
imp.setC(info.get_mosaic_labeled_ch())
IJ.run("Enhance Contrast", "saturated=0.35")
zcrop_imp, z_lims = z_crop(imp)
info.set_z_crop_frames(z_lims)
info.set_mosaic_labeled_ch(imp.getC())
IJ.setTool("rect")
zcrop_imp.hide()
imp2 = ZProjector.run(zcrop_imp, "max")
imp2.show()
imp2.setC(info.get_mosaic_labeled_ch())
crop_roi = None
while crop_roi is None:
WaitForUserDialog("Select XY region to crop...").show()
crop_roi = imp2.getRoi()
if crop_roi.getType():
info.set_xy_crop_rect(
str([(x, y) for x, y in zip(crop_roi.getPolygon().xpoints,
crop_roi.getPolygon().ypoints)]))
else:
info.set_xy_crop_rect(crop_roi.getBounds().toString())
imp2.close()
zcrop_imp.show()
zcrop_imp.setRoi(crop_roi)
IJ.run("Crop", "")
if crop_roi.getType():
IJ.run(zcrop_imp, "Make Inverse", "")
inv_roi = zcrop_imp.getRoi()
IJ.run(zcrop_imp, "Set...", "value=0 stack")
IJ.run(zcrop_imp, "Make Inverse", "")
# zcrop_imp = z_crop_finetune(zcrop_imp, info);
return imp, zcrop_imp, info, info.get_input_file_path()
def images_to_frames_stack(imgdir, savestack=False):
'''
Method for preparing a stack of frames using images inside the input folder.
When savestack is true it saves the resulting stack to the images folder while opening the stack.
'''
title = "tracing_stack.tiff" # Title of the final image stack.
imgdir = imgdir.getPath()
imglist = buildList(imgdir, ext)
if not imglist:
raise IOError("No {0} were found in {0}.".format(ext, imgdir))
method = "max"
implist = []
for img in imglist:
imp = ImagePlus(img)
if imp.isStack():
imp = ZProjector.run(imp, method)
implist.append(imp)
stack = ImageStack(
implist[0].getWidth(),
implist[0].getHeight())
[stack.addSlice(img.getProcessor()) for img in implist]
stackimp = ImagePlus(title, stack)
IJ.run(stackimp, "Properties...", "slices=1 frames={0}".format(stackimp.getStackSize()))
if savestack:
IJ.log("# Saving tracing stack...")
save_string = os.path.join(imgdir, title)
fs = ThreadedFileSaver.ThreadedFileSaver(stackimp, save_string, "saveAsTiff")
fs.start()
stackimp.show()
def stackprocessor(path, nChannels=4, nSlices=1, nFrames=1):
imp = ImagePlus(path)
imp = HyperStackConverter().toHyperStack(imp,
nChannels, # channels
nSlices, # slices
nFrames) # frames
imp = ZProjector.run(imp, "max")
return imp
def maxZprojection(stackimp):
'''copied from EMBL CMCI python-ImageJ cookbook.'''
zp = ZProjector(stackimp)
zp.setMethod(ZProjector.MAX_METHOD)
zp.doProjection()
zpimp = zp.getProjection()
return zpimp
def __favg(self) : zp = ZProjector(self.__impRes) zp.setMethod(ZProjector.AVG_METHOD) zp.doProjection() imp = zp.getProjection() imp.show() if self.__fire : IJ.run(imp, "Fire", "")
def main():
root = myDir.getPath() # get the root out the java file object
print(root)
import os, glob
# set up bioformats
from loci.plugins import BF
from loci.plugins.in import ImporterOptions
options = ImporterOptions()
options.setColorMode(ImporterOptions.COLOR_MODE_COMPOSITE)
options.setGroupFiles(True) # if the files are named logically if will group them into a stack
# this will do the maximum intensity projection
from ij.plugin import ZProjector
Zproj = ZProjector()
for path, subdirs, files in os.walk(root):
print(path)
# just get the one of the files that matches your image pattern
flist = glob.glob(os.path.join(path,"*.tif"))
print(len(flist))
if( flist ):
file = flist[0]
print("Processing {}".format(file))
options.setId(file)
imp = BF.openImagePlus(options)[0]
# show the image if you want to see it
IJ.run(imp, "Grays", "")
imp.show()
imp_max = Zproj.run(imp,'max')
IJ.run(imp_max, "Grays", "")
imp_max.show()
# save the Z projection
IJ.save(imp_max,file.rsplit('_',1)[0]+'_processed.tif')
def create_and_save(imp, projections, path, filename, export_format):
"""Wrapper to create one or more projections and export the results.
Parameters
----------
imp : ij.ImagePlus
The image stack to create the projections from.
projections : list(str)
A list of projection types to be done, valid options are 'Average',
'Maximum' and 'Sum'.
path : str
The path to store the results in. Existing files will be overwritten.
filename : str
The original file name to derive the results name from.
export_format : str
The suffix to be given to Bio-Formats, determining the storage format.
Returns
-------
bool
True in case projections were created, False otherwise (e.g. if the
given ImagePlus is not a Z-stack).
"""
if not projections:
log.debug("No projection type requested, skipping...")
return False
if imp.getDimensions()[3] < 2:
log.error("ImagePlus is not a z-stack, not creating any projections!")
return False
command = {
"Average": "avg",
"Maximum": "max",
"Sum": "sum",
}
for projection in projections:
log.debug("Creating '%s' projection...", projection)
proj = ZProjector.run(imp, command[projection])
export_using_orig_name(
proj,
path,
filename,
"-%s" % command[projection],
export_format,
overwrite=True,
)
proj.close()
return True
def getPreview(image):
enhancer = ContrastEnhancer()
projector = ZProjector()
splitter = ChannelSplitter()
imp1 = ImagePlus("CH1", )
width, height, channels, slices, frames = image.getDimensions()
chimps = []
for ch in range(1, channels + 1):
projector = ZProjector(ImagePlus("C%i" % ch, splitter.getChannel(image, ch)))
projector.setMethod(ZProjector.MAX_METHOD)
projector.doProjection()
proj = projector.getProjection()
enhancer.equalize(proj)
chimps.append(proj)
return RGBStackMerge.mergeChannels(chimps, False)
def BackgroundFilter(imp, projection_method = "Median"):
title = imp.getTitle()
#Make a dict containg method_name:const_fieled_value pairs for the projection methods
methods_as_strings=['Average Intensity', 'Max Intensity', 'Min Intensity', 'Sum Slices', 'Standard Deviation', 'Median']
methods_as_const=[ZProjector.AVG_METHOD, ZProjector.MAX_METHOD, ZProjector.MIN_METHOD, ZProjector.SUM_METHOD, ZProjector.SD_METHOD, ZProjector.MEDIAN_METHOD]
method_dict=dict(zip(methods_as_strings, methods_as_const))
#The Z-Projection magic happens here through a ZProjector object
zp = ZProjector(imp)
zp.setMethod(method_dict[projection_method])
zp.doProjection()
outstack = imp.createEmptyStack()
outstack.addSlice(zp.getProjection().getProcessor())
imp2 = ImagePlus(title+'_'+projection_method, outstack)
out = ImageCalculator().run("Subtract create 32-bit stack", imp, imp2)
return out
def average(imp):
"""Create an average intensity projection.
Parameters
----------
imp : ij.ImagePlus
The input stack to be projected.
Returns
-------
ij.ImagePlus
The result of the projection.
"""
if imp.getDimensions()[3] < 2:
log.warn("ImagePlus is not a z-stack, not creating a projection!")
return imp
log.debug("Creating average projection...")
proj = ZProjector.run(imp, "avg")
return proj
def previewImage(self, imp):
roi = imp.getRoi()
splitter = ChannelSplitter()
channels = []
for c in range(1, imp.getNChannels() + 1):
channel = ImagePlus("Channel %i" % c, splitter.getChannel(imp, c))
projector = ZProjector(channel)
projector.setMethod(ZProjector.MAX_METHOD)
projector.doProjection()
channels.append(projector.getProjection())
image = RGBStackMerge.mergeChannels(channels, False)
image.title = imp.title + " MAX Intensity"
image.luts = imp.luts
imp.setRoi(roi)
return image
def process_caspase_signal(path_signal, path_imp, path_imp_out):
path_imp = path_signal + path_imp
imp = IJ.openImage(path_imp)
imp.show()
zp = ZProjector(imp)
zp.setMethod(ZProjector.AVG_METHOD)
zp.doProjection()
zpimp = zp.getProjection()
imp_sub = ImageCalculator().run("Subtract create stack", imp, zpimp)
imp_sub.show()
IJ.saveAs(imp_sub, "Tiff", path_signal + path_imp_out)
imp.changes = False
imp.close()
imp_sub.changes = False
imp_sub.close()
def extract_frame_process_roi(imp, frame, channel, process, background, roi, z_min, z_max, correct_only_xy):
# extract frame and channel
imp_frame = ImagePlus("", extract_frame(imp, frame, channel, z_min, z_max)).duplicate()
# check for roi and crop
if roi != None:
#print roi.getBounds()
imp_frame.setRoi(roi)
IJ.run(imp_frame, "Crop", "")
# subtract background
if background > 0:
#IJ.log("Subtracting "+str(background));
IJ.run(imp_frame, "Subtract...", "value="+str(background)+" stack");
# enhance edges
if process:
IJ.run(imp_frame, "Mean 3D...", "x=1 y=1 z=0");
IJ.run(imp_frame, "Find Edges", "stack");
# project into 2D
if imp_frame.getNSlices() > 1:
if correct_only_xy:
imp_frame = ZProjector.run( imp_frame, "avg");
# return
return imp_frame
def extract_frame_process_roi(imp, frame, roi, options):
# extract frame and channel
imp_frame = ImagePlus("", extract_frame(imp, frame, options['channel'], options['z_min'], options['z_max'])).duplicate()
# check for roi and crop
if roi != None:
#print roi.getBounds()
imp_frame.setRoi(roi)
IJ.run(imp_frame, "Crop", "")
# subtract background
if options['background'] > 0:
#IJ.log("Subtracting "+str(background));
IJ.run(imp_frame, "Subtract...", "value="+str(options['background'])+" stack");
# enhance edges
if options['process']:
IJ.run(imp_frame, "Mean 3D...", "x=1 y=1 z=0");
IJ.run(imp_frame, "Find Edges", "stack");
# project into 2D if we only want to correct the drift in x and y
if imp_frame.getNSlices() > 1:
if options['correct_only_xy']:
imp_frame = ZProjector.run(imp_frame, "avg");
# return
return imp_frame
def subtractzproject(imp, projectionMethod="Median"):
"""This function takes an input stack, and subtracts a projection from the
whole stack from each individual frame. Thereby, everything that is not moving
in a timeseries is filtered away.
Args:
imp (ImagePlus): An input stack as ImagePlus object.
projectionMethod (str, optional): Choose the projection method. Options are
'Average Intensity', 'Max Intensity', 'Min Intensity', 'Sum Slices', 'Standard Deviation', 'Median'.
Defaults to "Median".
Returns:
ImagePlus: The resulting stack.
"""
#Start by getting the active image window and get the current active channel and other stats
cal = imp.getCalibration()
title = imp.getTitle()
# Define a dictionary containg method_name:const_fieled_value pairs for the projection methods.
methods_as_strings = [
'Average Intensity', 'Max Intensity', 'Min Intensity', 'Sum Slices',
'Standard Deviation', 'Median'
]
methods_as_const = [
ZProjector.AVG_METHOD, ZProjector.MAX_METHOD, ZProjector.MIN_METHOD,
ZProjector.SUM_METHOD, ZProjector.SD_METHOD, ZProjector.MEDIAN_METHOD
]
method_dict = dict(zip(methods_as_strings, methods_as_const))
# Run Z-Projection.
zp = ZProjector(imp)
zp.setMethod(method_dict[projectionMethod])
zp.doProjection()
impMedian = zp.getProjection()
# Subtract Z-Projection and return output ImagePlus.
impout = ImageCalculator().run("Subtract create 32-bit stack", imp,
impMedian)
impout.setCalibration(cal)
return impout
def doprojection(self, title, onGPU=False):
'''
Run ij.plugin.Zprojector on image referenced by title using self.method as
projection method and saves the projection on self.savefolder.
'''
IJ.log("# Processing {0}...".format(title))
imp = self.load_image(title)
if onGPU:
projection = self.CLIJ2_max_projection(imp)
else:
projection = ZProjector.run(imp, self.method)
if self.savefolder:
save_string = os.path.join(self.savefolder, title)
try:
ij.io.FileSaver(projection).saveAsTiff(save_string)
IJ.log("{0}".format(save_string))
except:
IJ.log(
"ij.io.FileSaver raised an exception while trying to save img '{0}' as '{1}'.Skipping image."
.format(title, save_string))
else:
imp.close()
projection.show()
def saveMaxProject(self, destFolder=''):
channelNumber = 1
for imp in self.channelImp:
if not destFolder:
destFolder = os.path.join(self.enclosingPath, self.enclosingfolder + '_tif', 'max')
if not os.path.isdir(destFolder):
os.makedirs(destFolder)
# make max project
zp = ZProjector(imp)
zp.setMethod(ZProjector.MAX_METHOD)
zp.doProjection()
zimp = zp.getProjection()
# save
saveFile = 'max_' + os.path.splitext(self.filename)[0] + '_ch' + str(channelNumber) + '.tif'
savePath = os.path.join(destFolder, saveFile)
fs = FileSaver(zimp)
bPrintLog('saveMaxProject():' + savePath, 3)
fs.saveAsTiff(savePath)
channelNumber += 1
def processFile(filename, inDir, outDir, dichroics, mergeList):
if mergeList is None:
merge = False
else:
merge = True
filenameExExt = os.path.splitext(filename)[0]
filepath = inDir + filename
# parse metadata
reader = ImageReader()
omeMeta = MetadataTools.createOMEXMLMetadata()
reader.setMetadataStore(omeMeta)
reader.setId(filepath)
numChannels = reader.getSizeC()
numSlices = reader.getSizeZ()
numFrames = reader.getSizeT()
seriesCount = reader.getSeriesCount()
globalMetadata = reader.getGlobalMetadata()
seriesMetadata = reader.getSeriesMetadata()
objLensName = globalMetadata['- Objective Lens name #1']
areaRotation = float(seriesMetadata['area rotation #1'])
acquisitionValueRotation = float(seriesMetadata['acquisitionValue rotation #1'])
if 'regionInfo rotation #1' in seriesMetadata:
regionInfoRotation = float(seriesMetadata['regionInfo rotation #1'])
else:
regionInfoRotation = float(0)
totalRotation = areaRotation + regionInfoRotation
physSizeX = omeMeta.getPixelsPhysicalSizeX(0)
physSizeY = omeMeta.getPixelsPhysicalSizeY(0)
pxSizeX = physSizeX.value(UNITS.MICROM)
pxSizeY = physSizeY.value(UNITS.MICROM)
# log metadata
IJ.log("\nMETADATA")
#IJ.log("Filename: " + filepath)
IJ.log("Number of series: " + str(seriesCount))
IJ.log("Number of channels: " + str(numChannels))
IJ.log("Number of frames: " + str(numFrames))
IJ.log("Number of slices: " + str(numSlices))
IJ.log("Objective lens: " + objLensName)
IJ.log("FOV rotation: " + str(areaRotation))
IJ.log("ROI rotation: " + str(regionInfoRotation))
IJ.log("Total rotation: " + str(totalRotation))
IJ.log("Pixel size:")
IJ.log("\t\tX = " + str(physSizeX.value()) + " " + physSizeX.unit().getSymbol())
IJ.log("\t\tY = " + str(physSizeY.value()) + " " + physSizeY.unit().getSymbol())
if merge:
tifDir = outDir + "." + str(datetime.now()).replace(" ", "").replace(":", "") + "/"
if not os.path.exists(tifDir):
os.makedirs(tifDir)
IJ.log("\nCreated temporary folder: " + tifDir + "\n")
else:
IJ.log("Unable to create temporary folder!\n")
else:
tifDir = outDir + filenameExExt + "/"
if not os.path.exists(tifDir):
os.makedirs(tifDir)
IJ.log("\nCreated subfolder: " + tifDir + "\n")
else:
IJ.log("\nSubfolder " + tifDir + " already exists.\n")
# correct images
tifFilePaths = []
for i in range(numChannels):
ip = extractChannel(oirFile=filepath, ch=i)
if dichroics[i] == "DM1":
IJ.log("Channel " + str(i+1) + " was imaged using DM1, so no correction required.")
else:
offsets = getOffset(obj=objLensName,dm=dichroicDict[dichroics[i]])
xom = offsets['x']
yom = offsets['y']
if abs(totalRotation) > 0.1:
rotOff = rotateOffset(x=xom, y=yom, angle=-totalRotation)
xom = rotOff['x']
yom = rotOff['y']
xop = int(round(xom/pxSizeX))
yop = int(round(yom/pxSizeY))
IJ.log("Channel " + str(i+1) + " offsets")
IJ.log("\t\tMicrometres")
IJ.log("\t\t\t\tx = " + str(xom))
IJ.log("\t\t\t\ty = " + str(yom))
IJ.log("\t\tPixels")
IJ.log("\t\t\t\tx = " + str(xop))
IJ.log("\t\t\t\ty = " + str(yop))
IJ.run(ip, "Translate...", "x=" + str(-xop) + " y=" + str(-yop) + " interpolation=None stack")
tifFilePath = tifDir + filenameExExt + "_ch_"+str(i+1)+".tif"
tifFilePaths.append(tifFilePath)
if os.path.exists(tifFilePath):
IJ.log("\nOutput file exists: " + tifFilePath)
IJ.log("Rerun plugin choosing a different output folder")
IJ.log("or delete file and then rerun plugin.")
IJ.log("Image processing terminated!\n")
return
FileSaver(ip).saveAsTiff(tifFilePath)
if merge:
max_list = []
for i in range(len(mergeList)):
if mergeList[i] != None:
mergeList[i] = readSingleChannelImg(tifFilePaths[mergeList[i]])
channel = mergeList[i]#https://python.hotexamples.com/examples/ij.plugin/RGBStackMerge/mergeChannels/python-rgbstackmerge-mergechannels-method-examples.html
projector = ZProjector(channel)
projector.setMethod(ZProjector.MAX_METHOD)
projector.doProjection()
max_list.append(projector.getProjection())
merged = RGBStackMerge.mergeChannels(mergeList, False)
merged_max = RGBStackMerge.mergeChannels(max_list, False)
mergedChannelFilepath = outDir + filenameExExt + ".tif"
maxMergedChannelFilepath = outDir + filenameExExt + "_max.tif"
if os.path.exists(mergedChannelFilepath):
IJ.log("\nOutput file exists: " + mergedChannelFilepath)
IJ.log("Rerun plugin choosing a different output folder")
IJ.log("or delete file and then rerun plugin.")
IJ.log("Image processing terminated!\n")
FileSaver(merged).saveAsTiff(mergedChannelFilepath)
FileSaver(merged_max).saveAsTiff(maxMergedChannelFilepath)
for tf in tifFilePaths:
os.remove(tf)
os.rmdir(tifDir)
IJ.log("\nFinished processing file:\n" + filepath + "\n")
if merge:
IJ.log("Image file with channels aligned:\n" + outDir + filenameExExt + ".tif\n")
else:
IJ.log("Aligned images (one tiff file for each channel) can be found in:\n" + tifDir + "\n")
def maxZprojection(stackimp): zp = ZProjector(stackimp) zp.setMethod(ZProjector.MAX_METHOD) zp.doProjection() zpimp = zp.getProjection() return (zpimp)
def Zproj(stackimp,method,z_ind,z_range): """ Gets a single channel z-stack as imp and max project it using the provided method. stackimp(ImagePlus): a single channel z-stack as ImagePlus object z_index(int): The central stack number z_range(int): The total number of stacks surrounding the z_index to indclude """ from ij.plugin import ZProjector # imp= stackimp.duplicate() zp = ZProjector(stackimp) if method=="MAX": print "MAX" zp.setMethod(ZProjector.MAX_METHOD) elif method=="SUM": zp.setMethod(ZProjector.MAX_METHOD) zp.setStartSlice(z_ind-int(z_range/2)) zp.setStopSlice(z_ind+int(z_range/2)) zp.doProjection() zpimp = zp.getProjection() return zpimp
def make_projection(imp, method, slices):
z_prjor = ZProjector(imp)
prj_imp = z_prjor.run(imp, method, slices[0], slices[1])
return prj_imp
def process_pi_signal(path, position, unsynchronized=True):
if unsynchronized:
path_signal = path + "\\pi"
path_signal_before = path_signal + "\\before"
path_signal_after = path_signal + "\\after"
path_signal_merged = path_signal + "\\merged"
path_imp_before = path_signal_before + "\\pi_in-focusxy%sc1.tif" % position
path_imp_after = path_signal_after + "\\pixy%sc1.tif" % position
path_imp_merged = path_signal_merged + "\\merged.tif"
path_imp_merged_sub = path_signal_merged + "\\merged_sub.tif"
imp1 = IJ.openImage(path_imp_before)
imp1.show()
imp2 = IJ.openImage(path_imp_after)
imp2.show()
zp1 = ZProjector(imp1)
zp1.setMethod(ZProjector.AVG_METHOD)
zp1.doProjection()
zpimp1 = zp1.getProjection()
zp2 = ZProjector(imp2)
zp2.setMethod(ZProjector.AVG_METHOD)
zp2.doProjection()
zpimp2 = zp2.getProjection()
imp_sub1 = ImageCalculator().run("Subtract create stack", imp1, zpimp1)
imp_sub1.show()
imp_sub2 = ImageCalculator().run("Subtract create stack", imp2, zpimp2)
imp_sub2.show()
concatenate_files(imp1, imp2, path_imp_merged)
concatenate_files(imp_sub1, imp_sub2, path_imp_merged_sub)
else:
path_signal = path + "\\pi\\seq0002xy%sc1.tif" % position
path_sub = path + "\\pi\\sub.tif"
imp = IJ.openImage(path_signal)
imp.show()
zp = ZProjector(imp)
zp.setMethod(ZProjector.AVG_METHOD)
zp.doProjection()
zpimp = zp.getProjection()
imp_sub = ImageCalculator().run("Subtract create stack", imp, zpimp)
imp_sub.show()
IJ.saveAs(imp_sub, "Tiff", path_sub)
imp.changes = False
imp.close()
zpimp.changes = False
zpimp.close()
imp_sub.changes = False
imp_sub.close()
def project(img, method):
zp = ZProjector.run(img, method)
return zp
def Zproj(stackimp, method, z_ind, z_range):
# Gets a stack and max project it.
from ij.plugin import ZProjector
# imp= stackimp.duplicate()
zp = ZProjector(stackimp)
if method == "MAX":
print "MAX"
zp.setMethod(ZProjector.MAX_METHOD)
elif method == "SUM":
print "SUM"
zp.setMethod(ZProjector.MAX_METHOD)
print "+/-", int(z_range / 2), "of z-index", z_ind
zp.setStartSlice(z_ind - int(z_range / 2))
zp.setStopSlice(z_ind + int(z_range / 2))
zp.doProjection()
zpimp = zp.getProjection()
return zpimp
import os, sys
from ij import IJ
from ij.io import FileSaver
from loci.plugins import BF
from subprocess import call
from ij.plugin import ZProjector
try:
filepath = getArgument()
except Exception, e:
sys.exit(" no file " + e)
try:
imp = BF.openImagePlus(filepath)
image = imp[0]
zProj = ZProjector(image)
zProj.setMethod(zProj.MAX_METHOD)
zProj.doProjection()
imgMax = zProj.getProjection()
#imgMax.show()
FileSaver(imgMax).saveAsTiff(os.path.splitext(filepath)[0] + "_MAX.tif")
except Exception, e:
sys.exit(e)
except Exception, e:
sys.exit(e)
def main():
# setup
Prefs.blackBackground = True
params = Parameters()
params.load_last_params()
# select folders
if params.last_input_path is not None:
DirectoryChooser.setDefaultDirectory(params.last_input_path)
dc = DirectoryChooser("Choose root folder containing data for analysis")
input_folder = dc.getDirectory()
params.last_input_path = input_folder
if input_folder is None:
raise KeyboardInterrupt("Run canceled")
if params.last_output_path is not None:
DirectoryChooser.setDefaultDirectory(
os.path.dirname(params.last_output_path))
dc = DirectoryChooser("choose location to save output")
output_folder = dc.getDirectory()
timestamp = datetime.strftime(datetime.now(), '%Y-%m-%d %H-%M-%S')
output_folder = os.path.join(output_folder, (timestamp + ' output'))
params.last_output_path = output_folder
os.mkdir(output_folder)
analysis_mode = choose_analysis_mode(params)
params.last_analysis_mode = analysis_mode
params.persist_parameters()
# load image(s):
files_lst = [
f for f in os.listdir(input_folder) if os.path.splitext(f)[1] == '.tif'
]
out_statses = []
for f in files_lst:
print("Working on image {}...".format(os.path.splitext(f)[0]))
imp = IJ.openImage(os.path.join(input_folder, f))
metadata = import_iq3_metadata(
os.path.join(input_folder,
os.path.splitext(f)[0] + '.txt'))
imp = HyperStackConverter.toHyperStack(imp, 3,
imp.getNSlices() // 3, 1,
"Color")
imp = ZProjector.run(imp, "max")
imp.setC(3)
IJ.run(imp, "Blue", "")
IJ.run(imp, "Enhance Contrast", "saturated=0.35")
imp.setC(2)
IJ.run(imp, "Red", "")
IJ.run(imp, "Enhance Contrast", "saturated=0.35")
imp.setC(1)
IJ.run(imp, "Green", "")
IJ.run(imp, "Enhance Contrast", "saturated=0.35")
imp.show()
imp.setDisplayMode(IJ.COMPOSITE)
cal = imp.getCalibration()
cal.setUnit(metadata["y_unit"])
cal.pixelWidth = metadata["x_physical_size"]
cal.pixelHeight = metadata["y_physical_size"]
imp.setCalibration(cal)
if analysis_mode == "GFP intensity":
out_stats = gfp_analysis(imp, f, output_folder)
elif analysis_mode == "Manual":
out_stats = manual_analysis(imp, f, output_folder)
out_statses.extend(out_stats)
print("Current total number of cells identified: {}".format(
len(out_statses)))
# get # nuclei per "cell"
params.save_parameters_to_json(
os.path.join(output_folder, "parameters used.json"))
WaitForUserDialog(
"Done", "Done, having analysed {} cells in total!".format(
len(out_statses))).show()
return
# manual roi copied from z-projected version of this resliced image (add roi from z-proj to ROI manager, then add
# to resliced image)
imp.killRoi();
IJ.run(imp, "Reslice [/]...", "output=1.000 start=Top avoid");
rot_imp = IJ.getImage();
crop_roi = Roi(10, 0, rot_imp.getWidth()-20, rot_imp.getHeight());
rot_imp.setRoi(crop_roi);
rot_imp.crop();
rot_imp.show();
WaitForUserDialog("pause").show();
split_ch = ChannelSplitter().split(rot_imp);
mch_imp = split_ch[0];
egfp_imp = split_ch[1];
roi_imp = split_ch[2];
zproj_imp = ZProjector.run(roi_imp, "max");
IJ.setRawThreshold(zproj_imp, 33153, 65535, None);
IJ.run(zproj_imp, "Make Binary", "")
zproj_imp.show();
raise error;
IJ.run(zproj_imp, "Skeletonize", "");
IJ.run(zproj_imp, "Create Selection", "");
roi = zproj_imp.getRoi();
floatpoly = roi.getContainedFloatPoints();
roi = PolygonRoi(floatpoly, Roi.FREELINE);
zproj_imp.setRoi(roi);
WaitForUserDialog("pause").show();
#IJ.setTool("freeline");
#WaitForUserDialog("Draw a line").show();
#IJ.run(zproj_imp, "Fit Spline", "");
def zproj(imp): zpimp = ZP() zpimp.setImage(imp) zpimp.setMethod(zpimp.MAX_METHOD) zpimp.setStartSlice(1) zpimp.setStopSlice(imp.getNSlices()) zpimp.doHyperStackProjection(True) zpedimp = zpimp.getProjection() return zpedimp
def saveMaxProject(self, destFolder=''):
# ch1
if self.imp_ch1:
# make max project
zp = ZProjector(self.imp_ch1)
zp.setMethod(ZProjector.MAX_METHOD)
zp.doProjection()
zimp = zp.getProjection()
# save
fs = FileSaver(zimp)
bPrintLog('saveMaxProject():' + self.savePathMax_ch1, 3)
fs.saveAsTiff(self.savePathMax_ch1)
# ch2
if self.imp_ch2:
# make max project
zp = ZProjector(self.imp_ch2)
zp.setMethod(ZProjector.MAX_METHOD)
zp.doProjection()
zimp = zp.getProjection()
# save
fs = FileSaver(zimp)
bPrintLog('saveMaxProject():' + self.savePathMax_ch2, 3)
fs.saveAsTiff(self.savePathMax_ch2)
# ch1
if self.imp_ch3:
# make max project
zp = ZProjector(self.imp_ch3)
zp.setMethod(ZProjector.MAX_METHOD)
zp.doProjection()
zimp = zp.getProjection()
# save
fs = FileSaver(zimp)
bPrintLog('saveMaxProject():' + self.savePathMax_ch3, 3)
fs.saveAsTiff(self.savePathMax_ch3)
def main():
### debug ###############################################################
#print (sys.version_info);
#print(sys.path);
#file_path = "D:\\data\\Inverse blebbing\\MAX_2dpf marcksl1b-EGFP inj_TgLifeact-mCh_movie e4_split-bleb1.tif";
#output_root = "D:\\data\\Inverse blebbing\\output";
#from datetime import datetime
#timestamp = datetime.strftime(datetime.now(), '%Y-%m-%d %H-%M-%S');
#output_folder = os.path.join(output_root, (timestamp + ' output'));
#os.mkdir(output_folder);
########################################################################
# ensure consistent preference settings
Prefs.blackBackground = False;
# prompt user for input parameters
params = mbui.analysis_parameters_gui();
# prompt user for file locations
file_path, output_folder = mbio.file_location_chooser(params.input_image_path);
params.setInputImagePath(file_path);
params.setOutputPath(output_folder);
# get image file
import_opts, params = mbui.choose_series(file_path, params);
imps = bf.openImagePlus(import_opts);
imp = imps[0];
# catch unexpected image dimensions - for now, project in Z...:
if imp.getNSlices() > 1:
mbui.warning_dialog(["More than one Z plane detected.",
"I will do a maximum projection before proceeding",
"Continue?"]);
imp = ZProjector.run(imp,"max all");
params = mbio.get_metadata(params);
params.setCurvatureLengthUm(round(params.curvature_length_um / params.pixel_physical_size) * params.pixel_physical_size);
params.persistParameters();
IJ.run(imp, "Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");
imp.show();
if imp.getNChannels() > 1:
imp.setPosition(params.membrane_channel_number, 1, 1);
mbui.autoset_zoom(imp);
IJ.run("Enhance Contrast", "saturated=0.35");
# prompt user to select ROI
original_imp, crop_params = mbui.crop_to_ROI(imp, params);
if crop_params is not None:
params.perform_spatial_crop = True;
mbui.autoset_zoom(imp);
else:
params.perform_spatial_crop = False;
# prompt user to do time cropping
imp, start_end_tuple = mbui.time_crop(imp, params);
params.setTimeCropStartEnd(start_end_tuple);
repeats = 1;
inner_outer_comparisons = None;
if params.inner_outer_comparison:
inner_outer_comparisons = InnerOuterComparisonData();
repeats = 2;
IJ.selectWindow(imp.getTitle());
IJ.run("Enhance Contrast", "saturated=0.35");
for r in range(0, repeats):
calculated_objects = CalculatedObjects();
if params.time_crop_start_end[0] is not None:
calculated_objects.timelist = [idx * params.frame_interval for idx in range(params.time_crop_start_end[0], params.time_crop_start_end[1]+1)]
else:
calculated_objects.timelist = [idx * params.frame_interval for idx in range(imp.getNFrames())];
calculated_objects, params, split_channels = mbfs.generate_edges(imp, params, calculated_objects, (r+1)/repeats);
membrane_channel_imp = split_channels[0];
actin_channel_imp = split_channels[1];
segmentation_channel_imp = split_channels[2];
calculated_objects = mbfs.calculate_outputs(params,
calculated_objects,
split_channels,
repeat_fraction=(r+1)/repeats);
# output colormapped images and kymographs
fig_imp_list = mbfs.generate_and_save_figures(imp, calculated_objects, params, membrane_channel_imp, segmentation_channel_imp);
mbfs.save_csvs(calculated_objects, params);
params.saveParametersToJson(os.path.join(params.output_path, "parameters used.json"));
imp.changes = False;
IJ.setTool("zoom");
if params.close_on_completion or (params.inner_outer_comparison and r!=(repeats-1)):
for fig_imp in fig_imp_list:
fig_imp.close();
elif params.close_on_completion and (r==(repeats-1)):
imp.close();
if params.inner_outer_comparison:
tname = "Time, " + params.interval_unit;
output_folder = os.path.dirname(params.output_path);
profile = [[((inner, outer), (float(outer)/inner)) for inner, outer in zip(calculated_objects.inner_outer_data.inner_means, calculated_objects.inner_outer_data.outer_means)]];
mbio.save_profile_as_csv(profile,
os.path.join(output_folder, "Intensity ratios.csv"),
"outer/inner",
xname="inner",
yname="outer",
tname=tname,
time_list=calculated_objects.timelist);
sd_profile = [[((inner, outer), (float(outer)/inner)) for inner, outer in zip(calculated_objects.inner_outer_data.inner_sds, calculated_objects.inner_outer_data.outer_sds)]];
mbio.save_profile_as_csv(profile,
os.path.join(output_folder, "Intensity standard deviation ratios.csv"),
"outer sd/inner sd",
xname="inner sd",
yname="outer sd",
tname=tname,
time_list=calculated_objects.timelist);
return;
print 'Opening image', imageNPath impN = IJ.openImage( imageNPath ) impN.setRoi( ROI_xStart, ROI_yStart, ROI_xSize, ROI_ySize ) slices = impN.getNSlices() if ROI_zSize == 0: ROI_zSize = slices stack = impN.getStack() # crop(int x, int y, int z, int width, int height, int depth) impN.setStack( stack.crop( ROI_xStart, ROI_yStart, ROI_zStart, ROI_xSize, ROI_ySize, ROI_zSize ) ) #impN.setStack( stack.crop( ROI_xStart, ROI_yStart, 130, ROI_xSize, ROI_ySize, 220 ) ) #impN.setStack( stack.crop( ROI_xStart, ROI_yStart, 275, ROI_xSize, ROI_ySize, 1 ) ) fs = FileSaver( impN ) fs.saveAsTiff( imageNCroppedPath ) zp = ZProjector(impN) zp.setMethod( ZProjector.MAX_METHOD ) zp.doProjection() MIPimpN = zp.getProjection() #MIPimpN.show() if applyMembraneCropping == 1: imageMPath = membraneFolder + digit + appendix imageMCroppedPath = cropMembraneOutput + digit + appendix print 'Opening image', imageMPath impM = IJ.openImage( imageMPath ) impM.setRoi( ROI_xStart, ROI_yStart, ROI_xSize, ROI_ySize ) slices = impM.getNSlices() if ROI_zSize == 0: ROI_zSize = slices
def startTracking(filepath, fdir, ffile, filename):
outpath = fdir
troutpath = fdir + separator + ffile + separator + "tracked" + separator
stackoutpath = fdir + separator + ffile + separator + "stacks" + separator
pixwidth = 0.647
interval_sec = 600 #pr
if "141006" in fdir:
interval_sec = 600
elif "141117" in fdir:
interval_sec = 300
elif "141215" in fdir:
interval_sec = 300
if not os.path.isdir(outpath):
os.mkdir(outpath)
if not os.path.isdir(troutpath):
os.mkdir(troutpath)
if not os.path.isdir(stackoutpath):
os.mkdir(stackoutpath)
print 'filepath: ', filepath #pr
print 'fdir: ', fdir #pr
print 'ffile: ', ffile #pr
IJ.run("Image Sequence...",
"open=" + filepath + " file=" + filename + " sort")
#pr
#IJ.run("Image Sequence...", "open=" + filepath + " file=molm sort"); #pr
imp = WindowManager.getCurrentImage()
imptitle = imp.getTitle()
nframes = imp.getNSlices()
IJ.run(
imp, "Properties...", "channels=1 slices=1 frames=" + str(nframes) +
" unit=inch pixel_width=" + str(pixwidth) + " pixel_height=" +
str(pixwidth) + " voxel_depth=1.0000 frame=[" + str(interval_sec) +
" sec]")
IJ.run(imp, "Duplicate...", "title=" + imptitle + "_dup duplicate")
imp_dup = WindowManager.getImage(imptitle + "_dup")
IJ.run(imp_dup, "Gaussian Blur...", "sigma=50 stack")
ic = ImageCalculator()
imp_corr = ic.run("Divide create 32-bit stack", imp, imp_dup)
imp_corr.setTitle(imptitle + "_corrected")
imp_corr.show()
imp.changes = False
imp.close()
imp_dup.changes = False
imp_dup.close()
IJ.run(imp_corr, "8-bit", "")
IJ.run(
imp_corr, "Normalize Local Contrast",
"block_radius_x=100 block_radius_y=100 standard_deviations=1 stretch stack"
)
IJ.saveAs(imp_corr, "Tiff",
stackoutpath + separator + imptitle + "_corrected.tif")
IJ.run(imp_corr, "Duplicate...", "title=" + imptitle + "_bg duplicate")
imp_bg = WindowManager.getImage(imptitle + "_bg")
#Prefs.blackBackground = True;
IJ.setAutoThreshold(imp_bg, "MinError dark")
IJ.run(imp_bg, "Convert to Mask", "stack")
IJ.run(imp_bg, "Analyze Particles...",
"size=10000-Infinity show=Masks stack")
imp_bg.changes = False
imp_bg.close()
imp_bgmask = WindowManager.getImage("Mask of " + imptitle + "_bg")
ic = ImageCalculator()
imp_corr_wobg = ic.run("Subtract create stack", imp_corr, imp_bgmask)
imp_corr_wobg.setTitle(imptitle + "_corrected_womask")
imp_corr_wobg.show()
IJ.saveAs(imp_corr_wobg, "Tiff",
stackoutpath + separator + imptitle + "_corrected_womask.tif")
#pr
# pr: substract average frames
zp = ZProjector(imp_corr_wobg)
zp.setMethod(ZProjector.AVG_METHOD)
zp.doProjection()
zpimp = zp.getProjection()
zpimp.show()
imp_corr_wobg_sub = ImageCalculator().run("Subtract create stack",
imp_corr_wobg, zpimp)
imp_corr_wobg_sub.show()
#imp_corr_wobg.changes = False
#imp_corr_wobg.close()
# pr: subtract average frames (END)
IJ.saveAs(
imp_corr_wobg_sub, "Tiff", stackoutpath + separator + imptitle +
"_corrected_womask_substracted.tif")
#pr
IJ.saveAs(
zpimp, "Tiff",
stackoutpath + separator + imptitle + "_corrected_womask_avg.tif")
#commented out: pr
#IJ.saveAs(imp_corr_wobg, "Tiff", stackoutpath+separator+imptitle+"_corrected_womask.tif");
IJ.saveAs(imp_bgmask, "Tiff",
stackoutpath + separator + imptitle + "_bgmask.tif")
print(stackoutpath + separator + imptitle +
"_corrected_womask_substracted.tif")
print(stackoutpath + separator + imptitle + "_corrected_womask_avg.tif")
print(stackoutpath + separator + imptitle + "_bgmask.tif")
imp_corr.changes = False
imp_corr.close()
imp_bgmask.changes = False
imp_bgmask.close()
imp_corr_wobg.changes = False
imp_corr_wobg.close()
#imp_corr_wobg_sub.changes = False
#imp_corr_wobg_sub.close()
zpimp.changes = False
zpimp.close()
#IJ.log(System.getProperty("os.name"))
#IJ.log(fdir)
return imp_corr_wobg_sub
def main():
# Prepare directory tree for output.
indir = IJ.getDirectory("input directory")
outdir = IJ.getDirectory(".csv output directory")
c1dir = os.path.join(outdir, "Channel1")
c2dir = os.path.join(outdir, "Channel2")
c3dir = os.path.join(outdir, "Channel3")
c4dir = os.path.join(outdir, "Channel4")
channelsdir = os.path.join(outdir, "Channels")
if not os.path.isdir(c1dir):
os.mkdir(c1dir)
if not os.path.isdir(c2dir):
os.mkdir(c2dir)
if not os.path.isdir(c3dir):
os.mkdir(c3dir)
if not os.path.isdir(c4dir):
os.mkdir(c4dir)
if not os.path.isdir(channelsdir):
os.mkdir(channelsdir)
# Collect all file paths in the input directory
files = readdirfiles(indir)
# Initialize the results tables.
c1Results = ResultsTable()
c2Results = ResultsTable()
c3Results = ResultsTable()
c4Results = ResultsTable()
for file in files:
IJ.log("File: {}/{}".format(files.index(file) + 1, len(files)))
if file.endswith('.tif'):
# Open .tiff file as ImagePlus.
imp = Opener().openImage(file)
imp = ZProjector.run(imp, "max")
# imp = stackprocessor(file,
# nChannels=4,
# nSlices=7,
# nFrames=1)
channels = ChannelSplitter.split(imp)
name = imp.getTitle()
# For every channel, save the inverted channel in grayscale as .jpg.
for channel in channels:
IJ.run(channel, "Grays", "")
IJ.run(channel, "Invert", "")
jpgname = channel.getShortTitle()
jpgoutfile = os.path.join(channelsdir,
"{}.jpg".format(jpgname))
IJ.saveAs(channel.flatten(), "Jpeg", jpgoutfile)
IJ.run(channel, "Invert", "")
# OPTIONAL - Perform any other operations (e.g. crossexcitation compensation tasks) before object count.
c2name = channels[2].getTitle()
cal = channels[2].getCalibration()
channels[2] = ImagePlus(
c2name,
ImageCalculator().run("divide create 32-bit", channels[2],
channels[3]).getProcessor(
) # This removes AF647 bleed-through
)
channels[2].setCalibration(cal)
# Settings for channel1 threshold.
c1 = countobjects(channels[0],
c1Results,
threshMethod="Triangle",
subtractBackground=True,
watershed=True,
minSize=0.00,
maxSize=100,
minCirc=0.00,
maxCirc=1.00)
# Settings for channel2 threshold.
c2 = countobjects(channels[1],
c2Results,
threshMethod="RenyiEntropy",
subtractBackground=True,
watershed=False,
minSize=0.00,
maxSize=30.00,
minCirc=0.00,
maxCirc=1.00)
# Settings for channel3 threshold.
c3 = countobjects(channels[2],
c3Results,
threshMethod="RenyiEntropy",
subtractBackground=True,
watershed=False,
minSize=0.00,
maxSize=30.00,
minCirc=0.00,
maxCirc=1.00)
# Settings for channel4 threshold.
c4 = countobjects(channels[3],
c4Results,
threshMethod="RenyiEntropy",
subtractBackground=True,
watershed=False,
minSize=0.20,
maxSize=100.00,
minCirc=0.00,
maxCirc=1.00)
# Format filenames for thresholded .tiff files.
outfileC1 = os.path.join(c1dir, "threshold_c1_{}".format(name))
outfileC2 = os.path.join(c2dir, "threshold_c2_{}".format(name))
outfileC3 = os.path.join(c3dir, "threshold_c3_{}".format(name))
outfileC4 = os.path.join(c4dir, "threshold_c4_{}".format(name))
# Save thresholded .tiff files.
IJ.saveAs(c1.flatten(), "Tiff", outfileC1)
IJ.saveAs(c2.flatten(), "Tiff", outfileC2)
IJ.saveAs(c3.flatten(), "Tiff", outfileC3)
IJ.saveAs(c4.flatten(), "Tiff", outfileC4)
# Show results tables.
# c1Results.show("channel1")
# c2Results.show("channel2")
# c3Results.show("channel3")
# c4Results.show("channel4")
# Prepare results table filenames.
c1out = os.path.join(outdir, "channel1.csv")
c2out = os.path.join(outdir, "channel2.csv")
c3out = os.path.join(outdir, "channel3.csv")
c4out = os.path.join(outdir, "channel4.csv")
# Save results tables.
ResultsTable.save(c1Results, c1out)
ResultsTable.save(c2Results, c2out)
ResultsTable.save(c3Results, c3out)
ResultsTable.save(c4Results, c4out)
def glidingprojection(imp,
startframe=1,
stopframe=None,
glidingFlag=True,
no_frames_per_integral=3,
projectionmethod="Median"):
"""This function subtracts the gliding projection of several frames from the
input stack. Thus, everything which moves too fast is filtered away.
Args:
imp (ImagePlus): Input image as ImagePlus object.
startframe (int, optional): Choose a start frame. Defaults to 1.
stopframe (int, optional): Choose an end frame. Defaults to None.
glidingFlag (bool, optional): Should a gliding frame by frame projection be used? Defaults to True.
no_frames_per_integral (int, optional): Number of frames to project each integral. Defaults to 3.
projectionmethod (str, optional): Choose the projection method. Options are
'Average Intensity', 'Max Intensity', 'Min Intensity', 'Sum Slices', 'Standard Deviation', 'Median'. Defaults to "Median".
Raises:
RuntimeException: Start frame > stop frame.
Returns:
ImagePlus: The output stack.
"""
# Store some image properties.
cal = imp.getCalibration()
width, height, nChannels, nSlices, nFrames = imp.getDimensions()
title = imp.getTitle()
# Some simple sanity checks for input parameters.
if stopframe == None: stopframe = nFrames
if (startframe > stopframe):
IJ.showMessage("Start frame > Stop frame, can't go backwards in time!")
raise RuntimeException("Start frame > Stop frame!")
# If a subset of the image is to be projected, these lines of code handle that.
if ((startframe != 1) or (stopframe != nFrames)):
imp = Duplicator().run(imp, 1, nChannels, 1, nSlices, startframe,
stopframe)
# Define the number of frames to advance per step based on boolean input parameter glidingFlag.
if glidingFlag: frames_to_advance_per_step = 1
else: frames_to_advance_per_step = no_frames_per_integral
# Make a dict containg method_name:const_fieled_value pairs for the projection methods
methods_as_strings = [
'Average Intensity', 'Max Intensity', 'Min Intensity', 'Sum Slices',
'Standard Deviation', 'Median'
]
methods_as_const = [
ZProjector.AVG_METHOD, ZProjector.MAX_METHOD, ZProjector.MIN_METHOD,
ZProjector.SUM_METHOD, ZProjector.SD_METHOD, ZProjector.MEDIAN_METHOD
]
method_dict = dict(zip(methods_as_strings, methods_as_const))
# Initialize a ZProjector object and an empty stack to collect projections.
zp = ZProjector(imp)
zp.setMethod(method_dict[projectionmethod])
outstack = imp.createEmptyStack()
# Loop through all the frames in the image, and project that frame with the other frames in the integral.
for frame in range(1, nFrames + 1, frames_to_advance_per_step):
zp.setStartSlice(frame)
zp.setStopSlice(frame + no_frames_per_integral)
zp.doProjection()
outstack.addSlice(zp.getProjection().getProcessor())
# Create an image processor from the newly created Z-projection stack
# nFrames = outstack.getSize()/nChannels
impout = ImagePlus(
title + '_' + projectionmethod + '_' + str(no_frames_per_integral) +
'_frames', outstack)
impout = HyperStackConverter.toHyperStack(impout, nChannels, nSlices,
nFrames)
impout.setCalibration(cal)
return impout
def do_projection(self, channel, proj_type=None):
proj = ZProjector() ## create projection class
if proj_type is None:
if self.do_z[channel] == "MAX":
proj.setMethod(ZProjector.MAX_METHOD)
elif self.do_z[channel] == "AVG":
proj.setMethod(ZProjector.AVG_METHOD)
else:
print "Dont know how to project this way"
print "Just using a single slice for images!!"
return None
else:
if proj_type == "MAX":
proj.setMethod(ZProjector.MAX_METHOD)
elif proj_type == "AVG":
proj.setMethod(ZProjector.AVG_METHOD)
else:
print "Dont know how to project this way"
print "Just using a single slice for images!!"
return None
proj.setImage(self.stack_imps[channel])
proj.doProjection()
projection = proj.getProjection()
conv = ImageConverter(projection)
conv.convertToGray16()
conv.setDoScaling(False)
self.projections[channel] = projection
self.projections_done[channel] = self.do_z[channel]
def main():
# ensure consistent preference settings
Prefs.blackBackground = False
# get locations for previous and new outputs
params = Parameters()
params.loadLastParams()
output_folder_old, output_folder = mbio.rerun_location_chooser(
params.input_image_path)
params.loadParametersFromJson(
os.path.join(output_folder_old, 'parameters used.json'))
params.setOutputPath(output_folder)
# present user with the familiar setup UI, with options that don't make sense/aren't yet implemented disabled
params = mbui.analysis_parameters_gui(rerun_analysis=True, params=params)
# get original image file (for overlays etc.)
if not os.path.isfile(params.input_image_path):
mbui.warning_dialog([
"The original data can't be found at the location specified in saved parameters. ",
"(Possibly something as simple as a change in network drive mapping has occurred)",
"Please specify the location of the original image file..."
])
params.setInputImagePath(
mbio.input_file_location_chooser(params.output_path))
import_opts, params = mbui.choose_series(params.input_image_path, params)
imps = bf.openImagePlus(import_opts)
imp = imps[0]
if imp.getNSlices() > 1:
mbui.warning_dialog([
"More than one Z plane detected.",
"I will do a maximum projection before proceeding", "Continue?"
])
imp = ZProjector.run(imp, "max all")
params = mbio.get_metadata(params)
params.setCurvatureLengthUm(
round(params.curvature_length_um / params.pixel_physical_size) *
params.pixel_physical_size)
params.persistParameters()
IJ.run(imp, "Set Scale...", "distance=0 known=0 pixel=1 unit=pixel")
imp.show()
if imp.getNChannels() > 1:
imp.setPosition(params.membrane_channel_number, 1, 1)
mbui.autoset_zoom(imp)
IJ.run("Enhance Contrast", "saturated=0.35")
# prompt user to select ROI
original_imp = Duplicator().run(imp)
_, crop_params = mbui.crop_to_ROI(imp, params)
imp.show()
if crop_params is not None:
params.perform_spatial_crop = True
mbui.autoset_zoom(imp)
imp.updateAndDraw()
review_crop = mb.check_cropping(output_folder_old, params)
keep_crop = not review_crop
if review_crop:
keep_crop = mbui.crop_review()
if not keep_crop:
imp.changes = False
imp.close()
imp = original_imp
else:
original_imp.close()
else:
original_imp.close()
# prompt user to do time cropping
imp, start_end_tuple = mbui.time_crop(imp, params)
params.setTimeCropStartEnd(start_end_tuple)
# import edges
membrane_edges = mbio.load_qcd_edges2(
os.path.join(output_folder_old, "user_defined_edges.zip"))
mbio.save_qcd_edges2(membrane_edges, params.output_path)
calculated_objects = CalculatedObjects()
calculated_objects.membrane_edges = membrane_edges
if params.time_crop_start_end[0] is not None:
calculated_objects.timelist = [
idx * params.frame_interval
for idx in range(params.time_crop_start_end[0],
params.time_crop_start_end[1] + 1)
]
else:
calculated_objects.timelist = [
idx * params.frame_interval for idx in range(imp.getNFrames())
]
split_channels = mbfs.split_image_plus(imp, params)
membrane_channel_imp = split_channels[0]
actin_channel_imp = split_channels[1]
segmentation_channel_imp = None
if params.photobleaching_correction:
if os.path.isfile(
os.path.join(output_folder_old, 'binary_membrane_stack.tif')):
segmentation_binary_path = os.path.join(
output_folder_old, 'binary_membrane_stack.tif')
segmentation_channel_imp = IJ.openImage(segmentation_binary_path)
else:
segmentation_channel_imp = split_channels[2]
segmentation_channel_imp = mb.make_and_clean_binary(
segmentation_channel_imp, params.threshold_method)
split_channels[2] = segmentation_channel_imp
calculated_objects = mbfs.calculate_outputs(params, calculated_objects,
split_channels)
# output colormapped images and kymographs
fig_imp_list = mbfs.generate_and_save_figures(imp, calculated_objects,
params, membrane_channel_imp,
segmentation_channel_imp)
mbfs.save_csvs(calculated_objects, params)
params.saveParametersToJson(
os.path.join(params.output_path, "parameters used.json"))
imp.changes = False
IJ.setTool("zoom")
if params.close_on_completion:
for fig_imp in fig_imp_list:
fig_imp.close()
imp.close()
return
def maxZprojection(stackimp): zp = ZProjector(stackimp) zp.setMethod(ZProjector.MAX_METHOD) zp.doProjection() zpimp = zp.getProjection() return zpimp
