Critical_reorganization_of_adolescent_prefrontal_circuitry/code/morphology/PreProMainStack.m

function [MGwanted,MGvolume,res]=PreProMainStack(load_main,Animal,Cell,m,range,int,loadMainStack)

info  =  imfinfo(strcat(load_main,Animal,'\',Cell,'\',loadMainStack,'.tif'));   

MGstack = zeros(info(1).Width,info(1).Height, range(2) - range (1)+1);   

count=0;
for r=range(1):range(2)
    count=count+1;
    mg  =  imread(strcat(load_main,Animal,'\',Cell,'\',loadMainStack,'.tif'), r, 'Info', info);
    background  =  imopen(mg, strel('disk',50));
    mg  =  mg - background;
    MGstack(:,:,count)  =  mg;
    clear mg
end

[~, BWmg]  =  hysteresis3d(MGstack, 0.1, 0.5, 26); % thresholds the microglia image with lower threshold 0.1 and upper threshold 0.5 and segments it with connectivity of 26, only returns the hysteresis images (~negates first output)
clear MGstack
[MGstack]  =  ordfilt3D(BWmg,14); % filters the BW microglia stack for 26 neighbours
clear BWmg

[MGstack_label, MGnum]  =  bwlabeln (MGstack);% labels parts of one distinct microglia with one number
size_mg = sum(MGstack_label(:)== 1:MGnum); % sums up pixels with the same number (so pixels of each microglial part or microglia)

[MGvolume, idx] = max(size_mg);% returns the volume and the index of the highest pixel volume
if m==2
    size_mg(1,idx)=0;
    clear idx MGvolume
    [MGvolume, idx] = max(size_mg);
elseif m==3
    size_mg(1,idx)=0;
    clear idx MGvolume
    [MGvolume, idx] = max(size_mg);
    size_mg(1,idx)=0;
    clear idx MGvolume
    [MGvolume, idx] = max(size_mg);
end

MGwanted = (MGstack_label == idx);% makes stack from the original microglia stack but with only the desired microglia displayed as logical one (so only it is shown)

res.pixel_width_um = info(1).Width./info(1).XResolution;% enter your pixel width in um (get from info in .tif)
res.pixel_height_um = info(1).Height./info(1).YResolution; % enter your pixel heigth in um
res.pixel_depth_um = int; % enter the step size (slice thickness) in um

MGvolume = MGvolume* (res.pixel_width_um*res.pixel_height_um*res.pixel_depth_um);% calculates the volume in um of the microglia from the volume in pixels