uploading version 2 o Palm analysis

Figure2/palm-astrocytes/Version_2/Main_V2.m

+%% Collect Linux\Slurm metadata
+disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
+disp('Job is running on node:')
+[~, node] = system('hostname');
+disp(node)
+disp('Job is run by user:')
+[~, user] = system('whoami');
+disp(user)
+disp('Current slurm jobs of current user:')
+[~, sq] = system(['squeue -u ', user]);
+disp(sq)
+tic
+disp(['Start: ' datestr(now, 'yyyymmdd_HHMMSS')])
+disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
+
+
+%%
+defineThreshold = false;
+if defineThreshold
+    ThresholdData = load('/mnt/IrisHCS/Data/PatrycjaMulica/VimentinS100B/PKM_20201027_gfap_s100b_20x_TripA53TGCAstro_20201027_150933_out/data.mat');
+    ThresholdData = ThresholdData.Data;
+    Q75_S100Vec = ThresholdData.Q75_S100;
+    Q75_VimentinVec = ThresholdData.Q75_Vimentin;
+    figure
+    histogram(Q75_S100Vec, 1000, 'FaceColor', 'r')
+    hold on
+    histogram(Q75_VimentinVec, 1000,  'FaceColor', 'g')
+    legend({'S100', 'Vimentin'})
+end
+
+ThresholdS100 = 250;
+ThresholdVimentin = 250;
+
+%% Flags
+
+% delete(gcp('nocreate'))
+% myCluster = parcluster('local');
+% AvailableWorkers = myCluster.NumWorkers;
+% if AvailableWorkers >= 28
+%     pool = parpool(28)
+% else
+%     pool = parpool(1)
+% end
+
+addpath(genpath('/work/projects/lcsb_hcs/Library/hcsforge'))
+
+if ~exist('InPath') % if Inpath is provided  via command line, use that one
+    %InPath = '/work/projects/lcsb_hcs/Data/PatrycjaMulica/GFAPSF100beta/PKM_20200723_training_optimization_20200806_111823_in';
+    %InPath = '/mnt/AtlasHCS/YokogawaCV8000Standalone/CellPathfinder/Patrycja/PKM_20201027_gfap_s100b_20x_TripA53TGCAstro_20201027_150933/AssayPlate_PerkinElmer_CellCarrierUltra96';
+    InPath = '/mnt/IrisHCS/Data/PatrycjaMulica/SP_markers_Test_astro20XRep1andRep2_20230705_154918_in';
+end
+
+MesPath = ls([InPath, '/*.mes']); MesPath = MesPath(1:end-1); % remove line break
+MetaData = f_CV8000_getChannelInfo(InPath, MesPath);
+
+if ~exist('OutPath') % if Outpath is provided  via command line, use that one
+    %OutPath = '/work/projects/lcsb_hcs/Data/PatrycjaMulica/GFAPSF100beta/PKM_20200723_training_optimization_20200806_111823_out';
+    %OutPath = '/mnt/D/tmp20200211';
+    OutPath = '/mnt/IrisHCS/Data/PatrycjaMulica/SP_markers_Test_astro20XRep1andRep2_20230705_154918_out';
+end
+
+%% Prepare folders
+mkdir(OutPath)
+PreviewPath = [OutPath, filesep, 'Previews'];
+mkdir(PreviewPath)
+
+%% Log
+f_LogDependenciesLinux(mfilename, OutPath)
+
+
+%% Load Metadata
+ObjectsAll = {};
+%MetaData = f_CV8000_getChannelInfo(InPath, MesPath);
+InfoTable = MetaData.InfoTable{:};
+Wells = unique(InfoTable.Well);
+fieldProgress = 0;
+for w = 1:numel(Wells)
+    WellThis = Wells{w};
+    InfoTableThisWell = InfoTable(strcmp(InfoTable.Well, WellThis),:);
+    FieldsThisWell = unique(InfoTableThisWell.Field);
+    for f = 1:numel(FieldsThisWell)
+        fieldProgress = fieldProgress + 1;
+        FieldThis = FieldsThisWell{f};
+        InfoTableThisField = InfoTableThisWell(strcmp(InfoTableThisWell.Field, FieldsThisWell{f}),:);
+        ChannelsThisField =  unique(InfoTableThisField.Channel);
+        ImPaths = cell(1, numel(ChannelsThisField));
+        for c = 1:numel(ChannelsThisField)
+            ChannelThis = ChannelsThisField{c};
+            InfoTableThisChannel = InfoTableThisField(strcmp(InfoTableThisField.Channel,ChannelThis),:);
+            InfoTableThisChannel = sortrows(InfoTableThisChannel, 'Plane', 'ascend');
+            chThisPaths = cell(numel(ChannelsThisField),1);
+            for p = 1:height(InfoTableThisChannel)
+                chThisPaths{p} = InfoTableThisChannel{p, 'file'}{:};
+                %for t = 1:height()
+            end
+            ImPaths{c} = chThisPaths;
+            MesFile = MetaData.MeasurementSettingFileName;
+        end
+       FieldMetaData{fieldProgress} = {ImPaths, MesFile, Wells{w}, FieldsThisWell{f}};
+    end
+end
+
+disp('Debug point')
+FieldMetaDataTable = cell2table(vertcat(FieldMetaData{:}))
+
+for i = 1:numel(FieldMetaData)
+%parfor i = 1:numel(FieldMetaData)
+%parfor i = 1:2
+    try
+        i    
+        ch1files = sort(FieldMetaData{i}{1}{1});
+        ch1Collector = cellfun(@(x) imread(x), ch1files, 'UniformOutput', false);
+        ch1 = cat(3,ch1Collector{:}); % vol(ch1, 0, 2000) Hoechst
+    
+        ch2files = FieldMetaData{i}{1}{2};
+        ch2Collector = cellfun(@(x) imread(x), ch2files, 'UniformOutput', false);
+        ch2 = cat(3,ch2Collector{:}); % vol(ch2, 0, 800) GFAP deep red
+        
+        ch3files = FieldMetaData{i}{1}{3};
+        ch3Collector = cellfun(@(x) imread(x), ch3files, 'UniformOutput', false);
+        ch3 = cat(3,ch3Collector{:}); % vol(ch3, 0, 2000) Nestin 488
+
+        ch4files = FieldMetaData{i}{1}{4};
+        ch4Collector = cellfun(@(x) imread(x), ch4files, 'UniformOutput', false);
+        ch4 = cat(3,ch4Collector{:}); % vol(ch4, 0, 3000) CellMaskO
+        
+        MesFile = FieldMetaData{i}{2};
+        WellThis = FieldMetaData{i}{3};
+        FieldThis = FieldMetaData{i}{4};
+        
+        Objects = f_imageAnalysis(ch1, ch2, ch3, ch4, WellThis, FieldThis, MesFile, PreviewPath, ThresholdS100, ThresholdVimentin);
+        
+        ObjectsAll{i} = Objects;
+    catch
+       continue
+    end
+end
+
+Data = vertcat(ObjectsAll{:});
+save([OutPath, filesep, 'data.mat'], 'Data');
+writetable(Data, [OutPath, filesep, 'data.csv'])
+disp('Script completed successfully')

Figure2/palm-astrocytes/Version_2/f_LogDependenciesLinux_V2.m

+function [FileList] = f_LogDependenciesLinux(Name, SavePath)
+%Collect all upstream scripts and save them in a folder named Dependencies
+%   Name: Function or script name as string
+%   SavePath: 
+%   Example: f_LogDependencies('Workflow_RosellaLC3_BPF_Summary_20170313.m', 'S:\HCS_Platform\Data\JavierJarazo\Rosella\LC3\Analysis_20170323_143443')
+    
+    SavePath = [SavePath filesep 'Dependencies'];
+    mkdir(SavePath);
+    
+    %% Scan recursively %%
+    FileList = matlab.codetools.requiredFilesAndProducts(Name)';
+    %%%%%%%%%%%%%%%%%%%%%%
+    FileCount = size(FileList,1);
+
+    for i = 1:FileCount
+        FileThis = regexp(FileList{i}, '/.*/(.*)', 'tokens'); FileThis = FileThis{:}{:};
+        SavePathThisFile = [SavePath, filesep, FileThis];
+        copyfile(FileList{i}, SavePathThisFile);
+    end
+    
+end
+

Figure2/palm-astrocytes/Version_2/f_imageAnalysis_V2.m

+function [Objects] = f_imageAnalysis(ch1B, ch2DR, ch3G, ch4O, WellThis, FieldThis, MesFile, PreviewPath, ThresholdS100, ThresholdVimentin)
+%Summary is fine do previews and clean comments
+%UNTITLED Summary of this function goes here
+%   Detailed explanation goes here
+    Summary = table();
+
+    %% segment nuclei
+    chNuc = max(ch1B, [], 3); % imtool(chNuc, [])
+    chNucMed = medfilt2(chNuc); % imtool(chNucMed, [])
+    NucMask = chNucMed > 150; % imtool(NucMask, [])
+
+    %% segment cells on CellMask
+    chCellMask = max(ch4O, [], 3); % imtool(chCellMask, [])
+    chCellMaskMed = medfilt2(chCellMask); % imtool(chCellMaskMed, [])
+    CellMask = chCellMaskMed > 150; % imtool(CellMask, [])
+ 
+    %% Features
+    Objects = table();
+    Objects.Well = {WellThis};
+    Objects.Field = {FieldThis};
+    Objects.NucArea = sum(NucMask(:));
+    Objects.CellArea = sum(CellMask(:));
+    Objects.meanDeepRedInCellMask = mean(ch2DR(CellMask));
+    Objects.meanGreenInCellMask = mean(ch3G(CellMask));
+    
+    %% Previews
+
+    imSize = size(chNuc);
+    [BarMask, BarCenter] = f_barMask(100, 0.32393102760889064, imSize, imSize(1)-50, 50, 20);
+    %it(BarMask)
+    
+    BPreview = f_imoverlayIris(imadjust(max(ch1B,[],3), [0 0.03], [0 1]), BarMask, [1 1 1]);%imtool(BPreview)
+    DRPreview = f_imoverlayIris(imadjust(max(ch2DR,[],3), [0 0.03], [0 1]), BarMask, [1 1 1]);%imtool(DRPreview)
+    GPreview = f_imoverlayIris(imadjust(max(ch3G,[],3), [0 0.09], [0 1]), BarMask, [1 1 1]);%imtool(GPreview)
+    OPreview = f_imoverlayIris(imadjust(max(ch4O,[],3), [0 0.03], [0 1]), BarMask, [1 1 1]);%imtool(OPreview)
+    
+    NucPreview = f_imoverlayIris(imadjust(chNuc, [0 0.01], [0 1]), imdilate(bwperim(NucMask),strel('disk', 1)), [0 0 1]);
+    NucPreview = f_imoverlayIris(NucPreview, BarMask, [1 1 1]);
+    %imtool(NucPreview)
+    
+    CellMaskPreview = f_imoverlayIris(imadjust(chCellMask, [0 0.01], [0 1]), imdilate(bwperim(CellMask),strel('disk', 1)), [1 1 0]);
+    CellMaskPreview = f_imoverlayIris(CellMaskPreview, BarMask, [1 1 1]);
+    %imtool(CellMaskPreview)
+    
+    NucPreviewPath = [PreviewPath, filesep, WellThis, '_', FieldThis, '_Nuc.png'];
+    CellMaskPreviewPath = [PreviewPath, filesep, WellThis, '_', FieldThis, '_CellMask.png'];
+    BPreviewPath = [PreviewPath, filesep, WellThis, '_', FieldThis, '_B.png'];
+    DRPreviewPath = [PreviewPath, filesep, WellThis, '_', FieldThis, '_DR.png'];
+    GPreviewPath = [PreviewPath, filesep, WellThis, '_', FieldThis, '_G.png'];
+    OPreviewPath = [PreviewPath, filesep, WellThis, '_', FieldThis, '_O.png'];
+
+    imwrite(NucPreview, NucPreviewPath)
+    imwrite(CellMaskPreview, CellMaskPreviewPath)
+    imwrite(BPreview, BPreviewPath)
+    imwrite(DRPreview, DRPreviewPath)
+    imwrite(GPreview, GPreviewPath)
+    imwrite(OPreview, OPreviewPath)
+    
+end
+

Figure2/palm-astrocytes/Version_2/f_imoverlayIris_V2.m

+function OverlayRGB = f_imoverlayIris(Im, Mask, RGB)
+%IMOVERLAY Adds an overlay mask to a color image without using interactive/graphical Matlab funcctionality.
+%
+%   Recommended for Slurm sbatch runs
+%   Im has to be two dimensional
+%   Mask has to be twoo dimensional as well
+%   RGB is a red green blue vector with a range from 0 to 1 for example [1 0 0]
+%   Example: Im = im2uint16(rand(100)); Mask = Im > 30000; OverlayRGB = f_imoverlayIris(Im, Mask, [1 0.5 0]); imtool(OverlayRGB)
+
+    Mask = logical(Mask);
+    ImClass = class(Im);
+    switch ImClass
+        case 'uint8'
+            MaxPossible = (2^8)-1;
+        case 'uint16'
+            MaxPossible = (2^16)-1;
+        otherwise
+            disp('Please input the graytone image as uint8 or as uint16')
+            return
+    end
+    if size(Im, 3) == 1
+        ImR = Im;
+        ImG = Im;
+        ImB = Im;
+    else
+        ImR = Im(:,:,1);
+        ImG = Im(:,:,2);
+        ImB = Im(:,:,3);
+    end
+    ImR(Mask) = RGB(1) * MaxPossible;
+    ImG(Mask) = RGB(2) * MaxPossible;
+    ImB(Mask) = RGB(3) * MaxPossible;
+
+    OverlayRGB = cat(3, ImR, ImG, ImB);
+
+
+
+end
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