, 8-bit"); run
, sauvegarde=File.directory(
, File.makeDirectory(sauvegarde+"/r_"+title2)
, Opens the binary neurons image and removes on edges and less than minNeuron add to manager open
, Analyze Particles
, Opens the binary nuclei image open
, Removes Neurons and nuclei when more or less than one nucleus per neuron nROI=roiManager
, for (i=0;i<nROI;i++){ selectWindow
, Select
, // selection of neurons in ROImanager run
, the neuron } selectWindow
Results") ,
, Results")
, for (i=0;i<nResults;i++){ count=getResult("Count
, !=1) { // Fills neurons and nuclei when 0 or more than 1 nucleus connected_neurons=connected_neurons+count
, Nuclei");roiManager("Select
, Binneurons");roiManager("Select
Results"); run ,
, reset")
AND, Binneurons" ,
, Creates Image of cell bodies by dilating and opening the nuclei in neurons run
, Options
, BinaryConditionalDilate ", "mask=Dilated seed=Nuclei iterations=-1 white
, //removes small bodies after Opening saveAs("tiff
, Partie 2 : Quantification des paramètres morphométriques des neurones. macro "AutoNeuriteJ_partII [F1
, NB: the file selected must contain any other folders than those who will be analysed
, // Minimal length to be an axon (pixels) minNeurite=5
, // Minimal ratio between (mean primary neurite length) and (axonal length)--> Minimal ratio to be an axon getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour0, minute0, second, msec)
, How many conditions do you have to analyze?, defaultValue
, // Ask for the number of stack to be analysed path=newArray(nombre_condition)
Parameter settings") ,
Minimal size to be a Neurite, minNeurite ,
Minimal size to be an Axon ,
Ratio (Axon Length)/(Mean Neurites length) to be an Axon ,
, Dialog.show(
, minNeurite=Dialog.getNumber(
, minAxon=Dialog.getNumber(
, ratio=Dialog.getNumber(
, for (e=0; e<nombre_condition; e++) { // Ask for the directory of each stack to be analysed
, long_neurite=newArray(1000); type_neurite=newArray(1000)
, minAxon="+minAxon)
,
, // Trace a pruning protection around the neurite end setForegroundColor, vol.255, p.255
, Fill
, // Filling of the selected area
AND ,
, Fill
, Skeletonize")
, Analyze Skeleton (2D/3D), /Skeleton plugins run
, Results")
, Maximum Branch Length
, // Length between the nucleus and the end close(); close, Tagged Skeleton
BX", i); y=getCoordinate("BY ,
, // Gets coordinates nom="Neurone_"+j+"_Neurite"+i+1
, // Gets name for(k=i+1;k<Nb_pointes;k++) {
, // for each next neurite nom2="Neurone_"+j+"_Neurite"+k+1
, // Gets name selectWindow(nom2); run("Select None")
, selectWindow(nom);run
, // Selects Neurite i selectWindow(nom2)
, Restore Selection")
, // overlay of selected neurite i in the image neurite k getStatistics(area, mean);overlap=mean
, // Increase k type of neurite imageCalculator, p.2
, // Increase i type of neurite reDraws i without overlap imageCalculator
, } // end for(k=i+1;k<Nb_pointes;k++)
, // For mean length computation of primary for(i=0;i<Nb_pointes;i++){
, BX", i); y=getCoordinate("BY
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