, 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

. Ij and . Renameresults, 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

. }-}-selectwindow, Results"); run

, reset")

I. /neuron, 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)

. Dialog, Parameter settings")

. Dialog, Minimal size to be a Neurite, minNeurite

. Dialog, Minimal size to be an Axon

. Dialog, 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)

. .. Specify,

, // Trace a pruning protection around the neurite end setForegroundColor, vol.255, p.255

, Fill

, // Filling of the selected area

/. Imagecalculator, 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

. //-for-each-neurite-i-x=getcoordinate, 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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