def convertStackToRGB(img):
""" Convert individual color layers to a single RGB composite
"""
try:
RGBStackConverter.convertToRGB(img)
except:
pass
return img
def save_qc_image(imp, rois, output_path):
"""save rois overlaid on imp to output_path"""
imp.killRoi()
roim = RoiManager(False)
for roi in rois:
roim.addRoi(roi)
roim.runCommand("Show All with labels")
RGBStackConverter.convertToRGB(imp)
roim.moveRoisToOverlay(imp)
FileSaver(imp).saveAsTiff(output_path)
roim.runCommand("Show None")
roim.close()
def GenerateRGB(imp):
channels1 = imp.getNChannels();
slices1 = slices2 = imp.getNSlices();
frames1 = frames2 = imp.getNFrames();
c1 = imp.getChannel();
z1 = imp.getSlice();
t2 = imp.getFrame();
imp2 = imp.createHyperStack("title2", 1, slices2, frames2, 24)
RGBStackConverter().convertHyperstack(imp, imp2);
# imp2.show()
return imp2
impCircles.setDisplayRange(0, 1);
IJ.run(impSphereProjection, "8-bit", "");
IJ.run(impCircles, "8-bit", "");
stack = ImageStack(impSphereProjection.getWidth(), impSphereProjection.getHeight());
stack.addSlice(impSphereProjection.getProcessor());
stack.addSlice(impCircles.getProcessor());
tempImp = ImagePlus("Cylinder Maximum Projection + spots", stack);
tempImp = HyperStackConverter.toHyperStack(tempImp, 2, 1, 1);
if (tempImp.getNChannels() == 2):
tempImp.setC(1);
IJ.run(tempImp, "Magenta", "");
tempImp.setC(2);
tempImp.setDisplayRange(0, 1);
RGBStackConverter.convertToRGB(tempImp);
if (resultCylinderMaxProjection is None):
resultCylinderMaxProjection = tempImp;
else:
resultCylinderMaxProjection.setProcessor(tempImp.getProcessor());
resultCylinderMaxProjection.show();
resultCylinderMaxProjection.updateAndDraw();
# MIP
impMaxProjection = clijx.pull(maxProjection);
IJ.run(impMaxProjection, "Enhance Contrast", "saturated=0.35");
if (resultMaxProjection is None):
resultMaxProjection = impMaxProjection;
resultMaxProjection.setTitle("Maximum Z projection");
_filtered = [threshold(p) for p in chpx[i]] # filtered pixels
filtered.append(FloatProcessor(ip.width, ip.height, _filtered, None))
# save each channels
for i in range(3):
IJ.save(ImagePlus("filtered_%d" % i, filtered[i]),
dstpath[:-4] + '_%d' % i)
# add slices to new stack
stack_new = ImageStack(imp.width, imp.height)
for i in range(3):
stack_new.addSlice(None, filtered[i])
# new image (stack)
imp_new = ImagePlus("new", stack_new)
imp_new.show()
IJ.save(imp_new, dstpath[:-4] + '_stack.tif')
# new image (color)
mergeimp = RGBStackMerge.mergeChannels([
ImagePlus(None, filtered[0]),
ImagePlus(None, filtered[1]),
ImagePlus(None, filtered[2]), None, None, None, None
], False)
mergeimp.title = "filtered"
RGBStackConverter.convertToRGB(mergeimp)
mergeimp.show()
IJ.save(mergeimp, dstpath)
# open EM image as ImagePlus for merging channel
EM = ImagePlus(saveEMfilepath)
# split rLM image in different channels
saverLMpath = os.path.join(transformation_output, "rLM.tif")
rLM = IJ.openImage(saverLMpath)
R, G, B = ChannelSplitter.split(rLM)
# Merge channels
overlay = RGBStackMerge.mergeChannels(
[None, None, B, EM, None, None, None],
True) # Change R,G, B if the chromatin channel is a different one.
# If you want a different color for the chromatin in the overlay image, change the position of the letter R,G,B,
# e.g. [B, None, None, EM, None, None, None] for displaying chromatin in the red channel.
RGBStackConverter.convertToRGB(overlay)
# save overlay
saveoverlaypath = os.path.join(workdir, "overlay_EM_Chromatin.tif")
fs = FileSaver(overlay)
fs.saveAsTiff(saveoverlaypath)
print("(----- )overlay EM and rLM image done")
############################################ clean up
# copy important files into the working directory
os.remove(os.path.join(workdir, "EM.tif"))
shutil.move(os.path.join(transformation_output, "EM.tif"),
os.path.join(workdir, "SEM.tif"))
shutil.move(os.path.join(transformation_output, "rLM.tif"),
# imRed.show()
# imTL.show()
# stack=ij.ImageStack(imRed.width, imRed.height)
# stack.addSlice("red", imRed.getProcessor())
# stack.addSlice("green", imGreen.getProcessor())
# stack.addSlice("tl", imTL.getProcessor())
# imstack=ij.ImagePlus("Stack", stack)
imMerge=RGBStackMerge.mergeChannels([imRed, imGreen, None, imTL], True)
#The merged image is a composite with three seperate channels. For now, we just want to convert the thing to RGB and save it out.
RGBStackConverter.convertToRGB(imMerge)
saveFn=os.path.join(analysisPath, tlFn[-9:-7], 'Merge.jpg'
#imMerge.show()
if stack==None:
stack=Stack("MergedChannels", imMerge)
else:fiji
stack+=imMerge
FileSaver(imMerge).saveAsJpeg(saveFn)
stack.show()
---------- --- ----------------------------------------------------
2019-06-16 JRM Initial adaptation. Use the GIT_HOME environment
variable to get the start of the path
"""
import os
from ij import IJ, ImagePlus
from ij.plugin import RGBStackMerge, RGBStackConverter
# use a path relative to the GIT_HOME environment variable
git_home = os.getenv("GIT_HOME")
print(git_home)
# start clean
IJ.run("Close All")
# Load the R, G, and B color separation images. These were created
# using make_mandrill_256.py
impc1 = ImagePlus(git_home + "/tips/ImageJ/tif/mandrill_256_red.tif")
impc2 = ImagePlus(git_home + "/tips/ImageJ/tif/mandrill_256_green.tif")
impc3 = ImagePlus(git_home + "/tips/ImageJ/tif/mandrill_256_blue.tif")
# merge my three images
imp_merge = RGBStackMerge.mergeChannels([impc1, impc2, impc3], True)
# convert the composite image to the RGB image
RGBStackConverter.convertToRGB(imp_merge)
imp_merge.show()