diff --git a/myosoft-imcf_identify_fibers.py b/myosoft-imcf_identify_fibers.py
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+# this is a python rewrite of the original ijm published at
+# https://github.com/Hyojung-Choo/Myosoft/blob/Myosoft-hub/Scripts/central%20nuclei%20counter.ijm
+
+# IJ imports
+# TODO: are the imports RoiManager and ResultsTable needed when using the services?
+from ij import IJ, WindowManager as wm
+from ij.plugin import Duplicator, RoiEnlarger, RoiScaler
+from trainableSegmentation import WekaSegmentation
+from de.biovoxxel.toolbox import Extended_Particle_Analyzer
+
+# Bio-formats imports
+from loci.plugins import BF
+from loci.plugins.in import ImporterOptions
+
+# python imports
+import time
+import os
+
+#@ String (visibility=MESSAGE, value="<html><b> Welcome to Myosoft - identify fibers! </b></html>") msg1
+#@ File (label="Select directory with classifiers", style="directory") classifiers_dir
+#@ File (label="Select directory for output", style="directory") output_dir
+#@ File (label="Select image file", description="select your image") path_to_image
+#@ Boolean (label="close image after processing", description="tick this box when using batch mode", value=False) close_raw
+#@ String (visibility=MESSAGE, value="<html><b> Morphometric Gates </b></html>") msg2
+#@ Integer (label="Min Area [um²]", value=10) minAr
+#@ Integer (label="Max Area [um²]", value=6000) maxAr
+#@ Float (label="Min Circularity", value=0.5) minCir
+#@ Float (label="Max Circularity", value=1) maxCir
+#@ Float (label="Min solidity", value=0.0) minSol
+#@ Float (label="Max solidity", value=1) maxSol
+#@ Integer (label="Min perimeter [um]", value=5) minPer
+#@ Integer (label="Max perimeter [um]", value=300) maxPer
+#@ Integer (label="Min min ferret [um]", value=0.1) minMinFer
+#@ Integer (label="Max min ferret [um]", value=100) maxMinFer
+#@ Integer (label="Min ferret AR", value=0) minFAR
+#@ Integer (label="Max ferret AR", value=8) maxFAR
+#@ Float (label="Min roundess", value=0.2) minRnd
+#@ Float (label="Max roundess", value=1) maxRnd
+#@ String (visibility=MESSAGE, value="<html><b> Expand ROIS to match fibers </b></html>") msg3
+#@ Float (label="ROI expansion [microns]", value=1) enlarge
+#@ String (visibility=MESSAGE, value="<html><b> channel positions in the hyperstack </b></html>") msg5
+#@ Integer (label="Membrane staining channel number", style="slider", min=1, max=5, value=1) membrane_channel
+#@ Integer (label="sub-tiling to economize RAM", style="slider", min=1, max=8, value=4) tiling_factor
+#@ ResultsTable rt
+#@ RoiManager rm
+
+
+def fix_ij_options():
+ """put IJ into a defined state
+ """
+ # disable inverting LUT
+ IJ.run("Appearance...", " menu=0 16-bit=Automatic")
+ # set foreground color to be white, background black
+ IJ.run("Colors...", "foreground=white background=black selection=red")
+ # black BG for binary images and pad edges when eroding
+ IJ.run("Options...", "black pad")
+ # set saving format to .txt files
+ IJ.run("Input/Output...", "file=.txt save_column save_row")
+ # ============= DON’T MOVE UPWARDS =============
+ # set "Black Background" in "Binary Options"
+ IJ.run("Options...", "black")
+ # scale when converting = checked
+ IJ.run("Conversions...", "scale")
+
+
+def fix_ij_dirs(path):
+ """use forward slashes in directory paths
+
+ Parameters
+ ----------
+ path : string
+ a directory path obtained from dialogue or script parameter
+
+ Returns
+ -------
+ string
+ a more robust path with forward slashes as separators
+ """
+
+ fixed_path = str(path).replace("\\", "/")
+ fixed_path = fixed_path + "/"
+
+ return fixed_path
+
+
+def open_image_with_BF(path_to_file):
+ """ use Bio-Formats to opens the first image from an image file path
+
+ Parameters
+ ----------
+ path_to_file : string
+ path to the image file
+
+ Returns
+ -------
+ ImagePlus
+ the first imp stored in a give file
+ """
+ options = ImporterOptions()
+ options.setColorMode(ImporterOptions.COLOR_MODE_GRAYSCALE)
+ options.setAutoscale(True)
+ options.setId(path_to_file)
+ imps = BF.openImagePlus(options) # is an array of ImagePlus
+
+ return imps[0]
+
+
+def fix_BF_czi_imagetitle(imp):
+ image_title = os.path.basename( imp.getTitle() )
+ image_title = image_title.replace(".czi", "")
+ image_title = image_title.replace(" ", "_")
+ image_title = image_title.replace("_-_", "")
+ image_title = image_title.replace("__", "_")
+ image_title = image_title.replace("#", "Series")
+
+ return image_title
+
+
+def clear_ij_roi_manager(rm):
+ """delete all ROIs from the RoiManager
+
+ Parameters
+ ----------
+ rm : RoiManager
+ a reference of the IJ-RoiManager
+ """
+ rm.runCommand('reset')
+
+
+def preprocess_membrane_channel(imp):
+ """apply myosoft pre-processing steps for the membrane channel
+
+ Parameters
+ ----------
+ imp : ImagePlus
+ a single channel image of the membrane staining
+ """
+ IJ.run(imp, "Enhance Contrast", "saturated=0.35")
+ IJ.run(imp, "Apply LUT", "")
+ IJ.run(imp, "Enhance Contrast", "saturated=1")
+ IJ.run(imp, "8-bit", "")
+ IJ.run(imp, "Invert", "")
+ IJ.run(imp, "Convolve...", "text1=[-1.0 -1.0 -1.0 -1.0 -1.0\n-1.0 -1.0 -1.0 -1.0 0\n-1.0 -1.0 24.0 -1.0 -1.0\n-1.0 -1.0 -1.0 -1.0 -1.0\n-1.0 -1.0 -1.0 -1.0 0] normalize")
+
+
+def apply_weka_model(model_path, imp, tiles_per_dim):
+ """apply a pretrained WEKA model to an ImagePlus
+
+ Parameters
+ ----------
+ model_path : string
+ path to the model file
+ imp : ImagePlus
+ ImagePlus to apply the model to
+ tiles_per_dim : integer
+ tiles the imp to save RAM
+
+ Returns
+ -------
+ ImagePlus
+ the result of the WEKA segmentation. One channel per class.
+ """
+ segmentator = WekaSegmentation()
+ segmentator.loadClassifier( model_path )
+ result = segmentator.applyClassifier( imp, [tiles_per_dim, tiles_per_dim], 0, True ) #ImagePlus imp, int[x,y,z] tilesPerDim, int numThreads (0=all), boolean probabilityMaps
+
+ return result
+
+
+def process_weka_result(imp):
+ """apply myosoft pre-processing steps for the imp after WEKA classification to prepare it
+ for ROI detection with the extended particle analyzer
+
+ Parameters
+ ----------
+ imp : ImagePlus
+ a single channel (= desired class) of the WEKA classification result imp
+ """
+ IJ.run(imp, "8-bit", "")
+ IJ.run(imp, "Median...", "radius=3")
+ IJ.run(imp, "Gaussian Blur...", "sigma=2")
+ IJ.run(imp, "Auto Threshold", "method=MaxEntropy")
+ IJ.run(imp, "Invert", "")
+
+
+def delete_channel(imp, channel_number):
+ """delete a channel from target imp
+
+ Parameters
+ ----------
+ imp : ImagePlus
+ the imp from which to delete target channel
+ channel_number : integer
+ the channel number to be deleted. starts at 0.
+ """
+ imp.setC(channel_number)
+ IJ.run(imp, "Delete Slice", "delete=channel")
+
+
+def run_extended_particle_analyzer( imp, eda_parameters ):
+ """identifies ROIs in target imp using the extended particle analyzer of the BioVoxxel toolbox
+ with given parameters
+
+ Parameters
+ ----------
+ imp : ImagePlus
+ the image on which to run the EPA on. Should be 8-bit thresholded
+ eda_parameters : array
+ all user defined parameters to restrict ROI identification
+ """
+ epa = Extended_Particle_Analyzer()
+ epa.readInputImageParameters(imp)
+ epa.setDefaultParameterFields()
+
+ # expose all parameters explicitly
+ epa.usePixel = False
+ epa.usePixelForOutput = False
+ epa.Area = str(eda_parameters[0]) + "-" + str(eda_parameters[1])
+ epa.Extent = "0.00-1.00"
+ epa.Perimeter = str(eda_parameters[2]) + "-" + str(eda_parameters[3])
+ epa.Circularity = str(eda_parameters[4]) + "-" + str(eda_parameters[5])
+ epa.Roundness = str(eda_parameters[6]) + "-" + str(eda_parameters[7])
+ epa.Solidity = str(eda_parameters[8]) + "-" + str(eda_parameters[9])
+ epa.Compactness = "0.00-1.00"
+ epa.AR = "0-Infinity"
+ epa.FeretAR = str(eda_parameters[10]) + "-" + str(eda_parameters[11])
+ epa.EllipsoidAngle = "0-180"
+ epa.MaxFeret = "0-Infinity"
+ epa.MinFeret = str(eda_parameters[12]) + "-" + str(eda_parameters[13])
+ epa.FeretAngle = "0-180"
+ epa.COV = "0.00-1.00"
+ epa.Output = "Nothing"
+ epa.Redirect = "None"
+ epa.Correction = "None"
+ epa.Reset = False
+ epa.DisplayResults = False
+ epa.ClearResults = False
+ epa.Summarize = False
+ epa.AddToManager = True
+ epa.ExcludeEdges = False
+ epa.IncludeHoles = False
+
+ epa.defineParticleAnalyzers()
+ epa.particleAnalysis( imp.getProcessor(), imp, imp.getTitle() )
+
+
+def measure_in_all_rois( imp, channel, rm ):
+ """measures in all ROIS on a given channel of imp all parameters that are set in IJ "Set Measurements"
+
+ Parameters
+ ----------
+ imp : ImagePlus
+ the imp to measure on
+ channel : integer
+ the channel to measure in. starts at 1.
+ rm : RoiManager
+ a reference of the IJ-RoiManager
+ """
+ imp.setC(channel)
+ rm.runCommand(imp,"Deselect")
+ rm.runCommand(imp,"Measure")
+
+
+def show_all_rois_on_image(rm, imp):
+ """shows all ROIs in the ROiManager on imp
+
+ Parameters
+ ----------
+ rm : RoiManager
+ a reference of the IJ-RoiManager
+ imp : ImagePlus
+ the imp on which to show the ROIs
+ """
+ imp.show()
+ rm.runCommand(imp,"Show All")
+
+
+def save_all_rois(rm, target):
+ """save all ROIs in the RoiManager as zip to target path
+
+ Parameters
+ ----------
+ rm : RoiManager
+ a reference of the IJ-RoiManager
+ target : string
+ the path in to store the ROIs. e.g. /my-images/resulting_rois.zip
+ """
+ rm.runCommand("Save", target)
+
+
+def enlarge_all_rois( amount_in_um, rm, pixel_size_in_um ):
+ """enlarges all ROIs in the RoiManager by x scaled units
+
+ Parameters
+ ----------
+ amount_in_um : float
+ the value by which to enlarge in scaled units, e.g 3.5
+ rm : RoiManager
+ a reference of the IJ-RoiManager
+ pixel_size_in_um : float
+ the pixel size, e.g. 0.65 px/um
+ """
+ amount_px = amount_in_um / pixel_size_in_um
+ all_rois = rm.getRoisAsArray()
+ rm.reset()
+ for roi in all_rois:
+ enlarged_roi = RoiEnlarger.enlarge(roi, amount_px)
+ rm.addRoi(enlarged_roi)
+
+
+def enhance_contrast( imp ):
+ """use "Auto" Contrast & Brightness settings in each channel of imp
+
+ Parameters
+ ----------
+ imp : ImagePlus
+ the imp on which to change C&B
+ """
+ for channel in range( imp.getDimensions()[2] ):
+ imp.setC(channel + 1) # IJ channels start at 1
+ IJ.run(imp, "Enhance Contrast", "saturated=0.35")
+
+
+def renumber_rois(rm):
+ """rename all ROIs in the RoiManager according to their number
+
+ Parameters
+ ----------
+ rm : RoiManager
+ a reference of the IJ-RoiManager
+ """
+ number_of_rois = rm.getCount()
+ for roi in range( number_of_rois ):
+ rm.rename( roi, str(roi + 1) )
+
+
+def setup_defined_ij(rm, rt):
+ """set up a clean and defined Fiji user environment
+
+ Parameters
+ ----------
+ rm : RoiManager
+ a reference of the IJ-RoiManager
+ rt : ResultsTable
+ a reference of the IJ-ResultsTable
+ """
+ fix_ij_options()
+ rm.runCommand('reset')
+ rt.reset()
+ IJ.log("\\Clear")
+
+
+execution_start_time = time.time()
+setup_defined_ij(rm, rt)
+
+# open image using Bio-Formats
+path_to_image = fix_ij_dirs(path_to_image)
+raw = open_image_with_BF(path_to_image)
+
+# get image info
+raw_image_calibration = raw.getCalibration()
+raw_image_title = fix_BF_czi_imagetitle(raw)
+
+# take care of paths and directories
+output_dir = fix_ij_dirs(output_dir)
+
+if not os.path.exists( str(output_dir + raw_image_title) ):
+ os.makedirs( str(output_dir + raw_image_title) )
+
+output_dir = str( output_dir + raw_image_title ) + "/"
+classifiers_dir = fix_ij_dirs(classifiers_dir)
+primary_model = classifiers_dir + "primary.model"
+secondary_model = classifiers_dir + "secondary_central_nuclei.model"
+
+# update the log for the user
+IJ.log( "Now working on " + str(raw_image_title) )
+if raw_image_calibration.scaled() == False:
+ IJ.log("Your image is not spatially calibrated! Size measurements are only possible in [px].")
+IJ.log( " -- settings used -- ")
+IJ.log( "area = " + str(minAr) + "-" + str(maxAr) )
+IJ.log( "perimeter = " + str(minPer) + "-" + str(maxPer) )
+IJ.log( "circularity = " + str(minCir) + "-" + str(maxCir) )
+IJ.log( "roundness = " + str(minRnd) + "-" + str(maxRnd) )
+IJ.log( "solidity = " + str(minSol) + "-" + str(maxSol) )
+IJ.log( "feret_ar = " + str(minFAR) + "-" + str(maxFAR) )
+IJ.log( "min_feret = " + str(minMinFer) + "-" + str(maxMinFer) )
+IJ.log( "ROI expansion [microns] = " + str(enlarge) )
+IJ.log( "sub-tiling = " + str(tiling_factor) )
+IJ.log( " -- settings used -- ")
+
+# image (pre)processing and segmentation (-> ROIs)
+membrane = Duplicator().run(raw, membrane_channel, membrane_channel, 1, 1, 1, 1) # imp, firstC, lastC, firstZ, lastZ, firstT, lastT
+preprocess_membrane_channel(membrane)
+weka_result1 = apply_weka_model(primary_model, membrane, tiling_factor )
+delete_channel(weka_result1, 1)
+weka_result2 = apply_weka_model(secondary_model, weka_result1, tiling_factor )
+delete_channel(weka_result2, 1)
+weka_result2.setCalibration(raw_image_calibration)
+process_weka_result(weka_result2)
+IJ.saveAs(weka_result2, "Tiff", output_dir + raw_image_title + "_all_fibers_binary")
+eda_parameters = [minAr, maxAr, minPer, maxPer, minCir, maxCir, minRnd, maxRnd, minSol, maxSol, minFAR, maxFAR, minMinFer, maxMinFer]
+raw.show() # EPA will not work if no image is shown
+run_extended_particle_analyzer(weka_result2, eda_parameters)
+
+# modify rois
+rm.hide()
+raw.hide()
+enlarge_all_rois( enlarge, rm, raw_image_calibration.pixelWidth )
+renumber_rois(rm)
+save_all_rois( rm, output_dir + "all_fiber_rois.zip" )
+
+# measure size & shape, save
+IJ.run("Set Measurements...", "area perimeter shape feret's redirect=None decimal=4")
+IJ.run("Clear Results", "")
+measure_in_all_rois( raw, membrane_channel, rm )
+rt.save(output_dir + "all_fibers_results.csv")
+
+# dress up the original image, save a overlay-png, present original to the user
+rm.show()
+raw.show()
+show_all_rois_on_image( rm, raw )
+raw.setDisplayMode(IJ.COMPOSITE)
+enhance_contrast( raw )
+IJ.run("From ROI Manager", "") # ROIs -> overlays so they show up in the saved png
+qc_duplicate = raw.duplicate()
+IJ.saveAs(qc_duplicate, "PNG", output_dir + raw_image_title + "_all_fibers")
+qc_duplicate.close()
+wm.toFront( raw.getWindow() )
+IJ.run("Remove Overlay", "")
+raw.setDisplayMode(IJ.GRAYSCALE)
+show_all_rois_on_image( rm, raw )
+total_execution_time_min = (time.time() - execution_start_time) / 60.0
+IJ.log("total time in minutes: " + str(total_execution_time_min))
+IJ.log( "~~ all done ~~" )
+IJ.selectWindow("Log")
+IJ.saveAs("Text", str(output_dir + raw_image_title + "_all_fibers_Log"))
+if close_raw == True:
+ raw.close()
\ No newline at end of file