def qc_background_regions(intensity_imp, bg_rois):
"""allow the user to view and correct automatically-determined background regions"""
imp = Duplicator().run(intensity_imp);
imp.setTitle("Background region QC");
imp.show();
imp.setPosition(1);
autoset_zoom(imp);
imp.setRoi(bg_rois[0]);
IJ.setTool("freehand");
notOK = True;
while notOK:
listener = UpdateRoiImageListener(bg_rois, is_area=True);
imp.addImageListener(listener);
dialog = NonBlockingGenericDialog("Background region quality control");
dialog.enableYesNoCancel("Continue", "Use this region for all t");
dialog.setCancelLabel("Cancel analysis");
dialog.addMessage("Please redraw background regions as necessary...")
dialog.showDialog();
if dialog.wasCanceled():
raise KeyboardInterrupt("Run canceled");
elif not(dialog.wasOKed()):
this_roi = imp.getRoi();
bg_rois = [this_roi for _ in listener.getRoiList()];
imp.removeImageListener(listener);
else:
last_roi = imp.getRoi();
qcd_bg_rois = listener.getRoiList();
if imp.getNFrames() > imp.getNSlices():
qcd_bg_rois[imp.getT() - 1] = last_roi;
else:
qcd_bg_rois[imp.getZ() - 1] = last_roi;
notOK = False;
imp.removeImageListener(listener);
imp.changes = False;
imp.close();
return qcd_bg_rois;
def get_no_nuclei_fully_enclosed(roi, full_nuclei_imp, overlap_threshold=0.65):
"""for a given cell roi and ImagePlus with binary nuclei, return how many nuclei lie ENTIRELY within the cell"""
bbox = roi.getBounds()
full_nuclei_imp.setRoi(roi)
cropped_nuc_imp = full_nuclei_imp.crop()
roi.setLocation(0, 0)
cropped_nuc_imp.setRoi(roi)
cropped_nuc_imp.killRoi()
roim = RoiManager(False)
mxsz = cropped_nuc_imp.getWidth() * cropped_nuc_imp.getHeight()
pa = ParticleAnalyzer(
ParticleAnalyzer.ADD_TO_MANAGER, ParticleAnalyzer.AREA
| ParticleAnalyzer.SLICE | ParticleAnalyzer.CENTROID, None, 0, mxsz)
pa.setRoiManager(roim)
pa.analyze(cropped_nuc_imp)
cell_imp = IJ.createImage("Cell binary", cropped_nuc_imp.getWidth(),
cropped_nuc_imp.getHeight(), 1, 8)
IJ.run(cell_imp, "Select All", "")
IJ.run(cell_imp, "Set...", "value=0 slice")
cell_imp.setRoi(roi)
IJ.run(cell_imp, "Set...", "value=255 slice")
no_enclosed_nuclei = 0
for idx, nuc_roi in enumerate(roim.getRoisAsArray()):
test_imp = Duplicator().run(cell_imp)
test_imp.setRoi(nuc_roi)
IJ.run(test_imp, "Set...", "value=255 slice")
test_imp.killRoi()
IJ.run(test_imp, "Create Selection", "")
IJ.run(test_imp, "Make Inverse", "")
test_roi = test_imp.getRoi()
test_roi_stats = test_roi.getStatistics()
cell_roi_stats = roi.getStatistics()
nuc_roi_stats = nuc_roi.getStatistics()
if test_roi_stats.area < (
cell_roi_stats.area +
(1 - overlap_threshold) * nuc_roi_stats.area
): # i.e. if more than (100*overlap_threshold)% of nucleus is inside cell...
no_enclosed_nuclei += 1
test_imp.changes = False
test_imp.close()
roi.setLocation(bbox.getX(), bbox.getY())
cropped_nuc_imp.changes = False
cropped_nuc_imp.close()
cell_imp.changes = False
cell_imp.close()
return no_enclosed_nuclei
class gui(JFrame):
def __init__(self): # constructor
#origing of coordinates
self.coordx = 10
self.coordy = 10
#inintialize values
self.Canvas = None
#create panel (what is inside the GUI)
self.panel = self.getContentPane()
self.panel.setLayout(GridLayout(9, 2))
self.setTitle('Subdividing ROIs')
#define buttons here:
self.Dapi_files = DefaultListModel()
mylist = JList(self.Dapi_files, valueChanged=self.open_dapi_image)
#mylist.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
mylist.setLayoutOrientation(JList.VERTICAL)
mylist.setVisibleRowCount(-1)
listScroller1 = JScrollPane(mylist)
listScroller1.setPreferredSize(Dimension(300, 80))
self.output_files = DefaultListModel()
mylist2 = JList(self.output_files)
#mylist.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
mylist2.setLayoutOrientation(JList.VERTICAL)
mylist2.setVisibleRowCount(-1)
listScroller2 = JScrollPane(mylist2)
listScroller2.setPreferredSize(Dimension(300, 80))
quitButton = JButton("Quit", actionPerformed=self.quit)
selectInputFolderButton = JButton("Select Input",
actionPerformed=self.select_input)
cubifyROIButton = JButton("Cubify ROI",
actionPerformed=self.cubify_ROI)
saveButton = JButton("Save ROIs", actionPerformed=self.save)
summsaveButton = JButton("Save Summary",
actionPerformed=self.save_summary)
self.textfield1 = JTextField('500')
#add buttons here
self.panel.add(listScroller1)
self.panel.add(listScroller2)
self.panel.add(selectInputFolderButton)
self.panel.add(Label("Adjust the size of the ROIs"))
self.panel.add(self.textfield1)
self.panel.add(cubifyROIButton)
self.panel.add(saveButton)
self.panel.add(summsaveButton)
self.panel.add(quitButton)
#self.panel.add(saveButton)
#self.panel.add(Zslider)
#other stuff to improve the look
self.pack() # packs the frame
self.setVisible(True) # shows the JFrame
self.setLocation(self.coordx, self.coordy)
#define functions for the buttons:
def quit(self, event): #quit the gui
self.dispose()
IJ.run("Close All")
def select_input(self, event):
self.input_path = IJ.getDirectory(
"Select Directory containing your data")
# get the files in that directory
self.input_files = listdir(self.input_path)
self.input_dapi = [s for s in self.input_files if "DAPI.tif" in s]
self.core_names = get_core_names(self.input_dapi)
# create output directory
self.output_path = path.join(
path.dirname(path.dirname(self.input_path)), "Cubified_ROIs")
if path.isdir(self.output_path):
print "Output path already created"
else:
mkdir(self.output_path)
print "Output path created"
# get the processed data
self.processed_files = listdir(self.output_path)
self.out_core_names = get_core_names(
get_core_names(self.processed_files)
) # needs the channel and roi to be removed
# populate the lists
for f in set(self.core_names):
if f not in set(self.out_core_names): # skip if processed
self.Dapi_files.addElement(f)
for f in set(self.out_core_names
): # a set so that only unique ones are shown
self.output_files.addElement(f)
def open_dapi_image(self, e):
sender = e.getSource()
IJ.run("Close All")
if not e.getValueIsAdjusting():
self.name = sender.getSelectedValue()
print self.name
dapi_filename = path.join(self.input_path, self.name + '_DAPI.tif')
#print dapi_filename
if not path.exists(dapi_filename):
print "I don't find the DAPI file, which is weird as I just found it before"
else:
#open stack and make the reslice
self.dapi_image = ImagePlus(dapi_filename) #read the image
# duplicate image to play with that one, and do the real processing in the background
self.imp_main = Duplicator().run(self.dapi_image)
self.imp_main.setTitle(self.name)
self.imp_main.show() #show image on the left
#self.original_image.getWindow().setLocation(self.coordx-self.original_image.getWindow().getWidth()-10,self.coordy-10) #reposition image
def cubify_ROI(self, e):
self.L = int(self.textfield1.text)
# get info
tit = self.imp_main.getTitle()
self.roi = self.imp_main.getRoi()
# get corners
corners = get_corners(self.roi, self.L)
self.corners_cleaned = clean_corners(corners, self.roi, self.L)
print 'found corners'
# get the overlay
self.ov = overlay_corners(self.corners_cleaned, self.L)
self.ov = overlay_roi(self.roi, self.ov)
# write roi name
self.ov = write_roi_numbers(self.ov, self.corners_cleaned, self.L)
# overlay
self.imp_main.setOverlay(self.ov)
self.imp_main.updateAndDraw()
def save(self, e):
# open the other channels
d1_filename = path.join(self.input_path, self.name + '_D1.tif')
d2_filename = path.join(self.input_path, self.name + '_D2.tif')
self.d1_image = ImagePlus(d1_filename) #read the image
print "d1 image opened"
self.d2_image = ImagePlus(d2_filename) #read the image
print "d2 image opened"
for image in [self.dapi_image, self.d1_image, self.d2_image]:
print "saving rois for image " + image.getTitle()
save_rois(image, self.corners_cleaned, self.L, self.output_path)
print "ROIs saved"
def save_summary(self, e):
IJ.selectWindow(self.name)
IJ.run("Flatten")
imp = IJ.getImage()
# downsample
# scale ENLARGING or SHRINKING the canvas dimensions
scale_factor = .2
new_width = str(int(imp.getWidth() * scale_factor))
new_height = str(int(imp.getHeight() * scale_factor))
IJ.selectWindow(self.name + "-1")
str_to_scale = "x=" + str(scale_factor) + " y=" + str(
scale_factor
) + " width=" + new_width + " height=" + new_height + " interpolation=Bilinear average create"
IJ.run("Scale...", str_to_scale)
# save
imp2 = IJ.getImage()
#IJ.saveAs("Tiff", path.join(OUTDIR, self.name + "_summaryOfROIs"))
IJ.saveAsTiff(
imp2, path.join(self.output_path,
self.name + "_summaryOfROIs.tif"))
print "summary image saved"
def do_angular_projection(imp,
max_r_pix=60,
min_r_pix=10,
generate_roi_stack=True):
"""perform ray-based projection of vessel wall, c.f. ICY TubeSkinner (Lancino 2018)"""
Prefs.blackBackground = True
print("do angular projection input imp = " + str(imp))
split_chs = ChannelSplitter().split(imp)
mch_imp = split_chs[0]
IJ.setAutoThreshold(mch_imp, "IsoData dark stack")
egfp_imp = split_chs[1]
proj_imp = Duplicator().run(egfp_imp)
cl_imp = split_chs[2]
if generate_roi_stack:
egfp_imp_disp = Duplicator().run(egfp_imp)
roi_stack = IJ.createImage("rois", egfp_imp.getWidth(),
egfp_imp.getHeight(), egfp_imp.getNSlices(),
16)
centres = []
projected_im_pix = []
ring_rois = []
for zidx in range(cl_imp.getNSlices()):
if ((zidx + 1) % 100) == 0:
print("Progress = " +
str(round(100 * (float(zidx + 1) / cl_imp.getNSlices()))))
projected_im_row = []
proj_imp.setZ(zidx + 1)
mch_imp.setZ(zidx + 1)
bp = mch_imp.createThresholdMask()
bp.dilate()
bp.erode()
bp.erode()
bp.erode()
mask_imp = ImagePlus("mask", bp)
IJ.run(mask_imp, "Create Selection", "")
roi = mask_imp.getRoi()
proj_imp.setRoi(roi)
IJ.run(proj_imp, "Set...", "value=0 slice")
IJ.run(proj_imp, "Make Inverse", "")
roi = proj_imp.getRoi()
centre = (roi.getStatistics().xCentroid, roi.getStatistics().yCentroid)
centres.append(centre)
ring_roi_xs = []
ring_roi_ys = []
for theta in range(360):
pt1 = (centre[0] + min_r_pix * math.cos(math.radians(theta)),
centre[1] + min_r_pix * math.sin(math.radians(theta)))
pt2 = (centre[0] + max_r_pix * math.cos(math.radians(theta)),
centre[1] + max_r_pix * math.sin(math.radians(theta)))
roi = Line(pt1[0], pt1[1], pt2[0], pt2[1])
proj_imp.setRoi(roi)
profile = roi.getPixels()
projected_im_row.append(max(profile))
try:
ring_roi_xs.append(roi.getContainedPoints()[profile.index(
max(profile))].x)
except IndexError:
ring_roi_xs.append(pt2[0])
try:
ring_roi_ys.append(roi.getContainedPoints()[profile.index(
max(profile))].y)
except IndexError:
ring_roi_ys.append(pt2[1])
proj_imp.killRoi()
ring_roi = PolygonRoi(ring_roi_xs, ring_roi_ys, Roi.FREELINE)
ring_rois.append(ring_roi)
if generate_roi_stack:
roi_stack.setZ(zidx + 1)
roi_stack.setRoi(ring_roi)
IJ.run(roi_stack, "Line to Area", "")
IJ.run(
roi_stack, "Set...",
"value=" + str(roi_stack.getProcessor().maxValue()) + " slice")
#egfp_imp.setRoi(ring_roi);
projected_im_pix.append(projected_im_row)
# for ch in split_chs:
# ch.close();
out_imp = ImagePlus(
"projected", FloatProcessor([list(x) for x in zip(*projected_im_pix)]))
if generate_roi_stack:
roi_stack.show()
egfp_imp_disp.show()
# merge?
else:
roi_stack = None
return out_imp, roi_stack, ring_rois, centres