Trial Multi0cell count display

Adjusted 3D display code for displaying multiple cell counter types.

.gitignore

@@ -2,3 +2,4 @@ data/*
 *.backup
 gen/*
 *.csv
+*.asv

src/_general/test_histology_pipeline.m

@@ -90,15 +90,18 @@
 % Extract results from ImageJ Cell Counter
 % --- Data specific ---
 cellcountpath = 'gen\cell-count\output\2023-141-09279\';
+slice_path = 'W:\AnalyzedData\Histology\2023-141-09279\downsampledImages\j3_old';
 cellcountpath = 'W:\AnalyzedData\Histology\2023-141-09279\CellCounterResults';
+slice_path = 'Z:\Falk Bronnle\DATA\Brain 02888-22007\TIFFS 10x\Slices';
+cellcountpath = 'Z:\Falk Bronnle\DATA\Brain 02888-22007\TIFFS 10x\Cellcount';
 % ---------------------
 [histology_points,slice_order] = AW_cellcounter2histology(slice_path,cellcountpath,resize_factor);
 
 % Convert points in histology images to CCF coordinates
 ccf_points = AP_histology2ccf(histology_points,slice_path);
 
 % Display points in 3D with brain mesh outline
-h_scatter = AW_view_celldistribution_volume(tv,cell2mat(ccf_points));
+h_scatter = AW_view_celldistribution_volume(tv,slice_order);
 
 
 % Concatenate points and round to nearest integer coordinate

src/summary/AW_cellcounter2histology.m

@@ -1,4 +1,4 @@
-function [histology_points,slice_order] = AW_cellcounter2histology(slice_path,cellcountpath,resize_factor)
+function [ccf_points,slice_order] = AW_cellcounter2histology(slice_path,cellcountpath,resize_factor)
 %
 % slice_path: path to folder that contains 
 %       1) downsampled images for alignment
@@ -7,31 +7,62 @@
 %       4) atlas2histology_tform.mat: from AP_histology
 
 
+% load slice_order data
+slice_order_fn = [slice_path filesep 'slice_order.csv'];
+slice_order = readtable(slice_order_fn);
+
 % load cell counter data
 cellcount_path_dir = dir([cellcountpath filesep '*.xml*']);
 cellcount_fn = natsortfiles(cellfun(@(path,fn) [path filesep fn], ...
     {cellcount_path_dir.folder},{cellcount_path_dir.name},'uni',false));
 n_cellcount = length(cellcount_fn);
 
-hist_points = cell(n_cellcount,1);
+    % preallocate cell arrays
+markers = cell(n_cellcount,1);
 im_fn = cell(n_cellcount,1);
-
+    % loop through all cell counter files
 for ii = 1:n_cellcount
-    [im_fn{ii},hist_points{ii}] = readImageJCellCount(cellcount_fn{ii});
-end
+    [im_fn{ii},markers{ii}] = readImageJCellCount(cellcount_fn{ii});
+    nTypes = length(markers{ii});
 
-% load slice_order data
-slice_order_fn = [slice_path filesep 'slice_order.csv'];
-slice_order = readtable(slice_order_fn);
+    % apply resize factor
+    for typeIdx = 1:nTypes     
+        markers{ii}(typeIdx).MarkerXY_rz = resize_factor*markers{ii}(typeIdx).MarkerXY;
+    end
 
-for ii = 1:n_cellcount 
+    % collect metadata (names, type #)
+    if ii == 1
+        markerIdx = [markers{ii}.Type];
+        markerNames = [markers{ii}.Name];
+    else
+        markerIdx = union([markers{ii}.Type],markerIdx,'stable');
+        markerNames = union([markers{ii}.Name],markerNames,'stable');
+    end
+
+    % add cell_counter file name to slice_order table
     im_num = find(ismember(slice_order.ori_filename,im_fn{ii}));
-%     resize_factor = slice_order.resize_factor(ii);
     if ~isempty(im_num)
-        slice_order.histology_points{im_num} = resize_factor*hist_points{ii};
         [~,name,ext] = fileparts(cellcount_fn{ii});
         slice_order.cellcount_fn{im_num} = [name,ext];
     end
 end
-histology_points = slice_order.histology_points;
+
+% allocate markers XY to table
+nTypes = length(markerNames);
+for ii = 1:n_cellcount
+    for tt = 1:nTypes
+        typeIdx = matches([markers{ii}.Name],markerNames(tt));
+        slice_order.(markerNames(tt)){ii} = markers{ii}(typeIdx).MarkerXY_rz;
+    end
+end
+
+% converting to CCF markers XY to table
+for tt = 1:nTypes
+    histology_points = slice_order.(markerNames(tt));
+    ccf_points_temp = AP_histology2ccf(histology_points,slice_path);
+    slice_order.(markerNames(tt)+"_ccf") = ccf_points_temp;
+end
+
+ccf_points = slice_order(:,endsWith(slice_order.Properties.VariableNames,'_ccf'));
+
 end

src/summary/AW_view_celldistribution_volume.m

@@ -1,8 +1,16 @@
-function h_scatter = AW_view_celldistribution_volume(tv,ccf_points_cat)
+function h_scatter = AW_view_celldistribution_volume(tv,slice_order)
 % AP_view_celldistribution_volume(tv,ccf_points_cat)
 %
 % Plot histology warped onto CCF volume
 
+ccf_points = slice_order(:,endsWith(slice_order.Properties.VariableNames,'_ccf'));
+nTypes = size(ccf_points,2);
+cellTypeNames = ccf_points.Properties.VariableNames;
+% if nTypes > 1
+%     disp(ColNames)
+%     typeIdx = input('which cell type do you want to plot?');
+% end
+
 
 % Create figure
 gui_fig = figure;
@@ -28,11 +36,21 @@
 
 % Draw all datapoints
 % ccf_points_cat is in native CCF order [AP/DV/ML] 
-h_scatter = scatter3(axes_atlas,ccf_points_cat(:,1),... % AP
-                    ccf_points_cat(:,3),... % ML
-                    ccf_points_cat(:,2),... % DV
-                    5,'red','filled','o');  
-
+Color = [ 1,0,0;...
+          0,1,0;...
+          0,0.5,1;...
+          1,0,1;];
+MrkrSz = 10;
+for typeIdx = 1:nTypes
+    ccf_points_cat = cell2mat(ccf_points.(cellTypeNames{typeIdx}));
+    h_scatter(typeIdx) = scatter3(axes_atlas,ccf_points_cat(:,1),... % AP
+                        ccf_points_cat(:,3),... % ML
+                        ccf_points_cat(:,2),... % DV
+                        MrkrSz,Color(typeIdx,:),'filled','o');  
+end
+
+    legend(["Brain",cellTypeNames],'Interpreter','none');
+end
 
 
 % % Attempt plotting as 3D surface

src/summary/readImageJCellCount.m

@@ -1,23 +1,40 @@
-function [im_fn,MarkerXY] = readImageJCellCount(filename,typeIdx)
+function [im_fn,Markers] = readImageJCellCount(filename)
 
-%% load XML
-
-S = readstruct(filename);
-% data structure
-% S -> ImageProperties
-%       ->
-%       ->
-% S.Marker_Data.Marker_Type: struct array of different marker types
-% S.Marker_Data.Marker_Type.Marker: 1xn struct array with fields:
-%    MarkerX
-%    MarkerY
-%    MarkerZ
-if ~exist('typeIdx','var') || isempty(typeIdx);typeIdx = 1;end
-
-im_fn = S.Image_Properties.Image_Filename;
-if isfield(S.Marker_Data.Marker_Type,'Marker')
-    MarkerXY = [ [S.Marker_Data.Marker_Type(typeIdx).Marker.MarkerX]',...
-             [S.Marker_Data.Marker_Type(typeIdx).Marker.MarkerY]' ];
-else
-    MarkerXY = NaN(0,2);
+    %% load XML
+
+    S = readstruct(filename);
+    % data structure
+    % S -> ImageProperties
+    %       ->
+    %       ->
+    % S.Marker_Data.Marker_Type: struct array of different marker types
+    % S.Marker_Data.Marker_Type.Marker: 1xn struct array with fields:
+    %    MarkerX
+    %    MarkerY
+    %    MarkerZ
+
+    im_fn = S.Image_Properties.Image_Filename;
+
+    Markers = struct;
+    nTypes = length(S.Marker_Data.Marker_Type);
+        for typeIdx = 1:nTypes 
+            Markers(typeIdx).Type = S.Marker_Data.Marker_Type(typeIdx).Type;
+            if isfield(S.Marker_Data.Marker_Type,'Name')
+                Markers(typeIdx).Name = S.Marker_Data.Marker_Type(typeIdx).Name;
+            else
+                Markers(typeIdx).Name = "";
+            end
+            Markers(typeIdx).MarkerXY = readCellType(S,typeIdx);
+        end
 end
+
+function MarkerXY = readCellType(S,typeIdx)
+    if ~exist('typeIdx','var') || isempty(typeIdx);typeIdx = 1;end
+    if isfield(S.Marker_Data.Marker_Type,'Marker') && ...
+            ~all(ismissing(S.Marker_Data.Marker_Type(typeIdx).Marker))
+        MarkerXY = [ [S.Marker_Data.Marker_Type(typeIdx).Marker.MarkerX]',...
+                 [S.Marker_Data.Marker_Type(typeIdx).Marker.MarkerY]' ];
+    else
+        MarkerXY = NaN(0,2);
+    end
+end