depth correction

Browsing Functions/accf2pxs_mm.m

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+function y_mm = accf2pxs_mm(x_mm)
+% convert Allen Common Coordinates into standard values (Paxinos and Franklin)
+% x_mm   Allen Common Coordinates
+%     if this is scaler, x_mm should be depth
+%     if this is n x 3 array, x_mm is an array of the same (or similar) size
+% y_mm Paxinos and Franklin coordinates
+
+if size(x_mm,2) ==1 
+    y_mm = 0.921 * x_mm - 0.834; % global
+    % y = 0.908 * x - 0.957; % local
+
+elseif size(x_mm,2) == 3
+    % assume that the 2nd column is the DV
+    y_mm = x_mm;
+    y_mm(:,2) = 0.921 * x_mm(:,2) - 0.834; % global
+    % y(:,2) = 0.908 * x(:,2) - 0.957;  % local
+
+else
+    error('unexpected size')
+end

Browsing Functions/allenCCF2pxs_mm.m

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+function y_mm = accf2pxs_mm(x_mm)
+% convert Allen Common Coordinates into standard values (Paxinos and Franklin)
+% x_mm   Allen Common Coordinates 
+% y_mm Paxinos and Franklin coordinates
+
+if size(x_mm,2) ==1 
+    y_mm = 0.921 * x_mm - 0.834; % global
+    % y = 0.908 * x - 0.957; % local
+
+elseif size(x_mm,2) == 3
+    % assume that the 2nd column is the DV
+    y_mm = x_mm;
+    y_mm(:,2) = 0.921 * x_mm(:,2) - 0.834; % global
+    % y(:,2) = 0.908 * x(:,2) - 0.957;  % local
+
+else
+    error('unexpected size')
+end

Browsing Functions/apdvml2info.m

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+function Tapdvml = apdvml2info(apdvml_points, av, st)
+% apdvml_points has three columns for ap, dv, and ml
+% bregma is 1 x 3 in size
+% atlas_resolution in mm
+% av  1320 ,800, 1140
+% st
+%
+% see also
+% Analyze_Clicked_Points.m
+
+% generate needed values
+bregma = allenCCFbregma(); % bregma position in reference data space
+atlas_resolution = 0.010; % mm
+
+
+ap = -(apdvml_points(:,1)-bregma(1))*atlas_resolution;
+dv = (apdvml_points(:,2)-bregma(2))*atlas_resolution;
+ml = (apdvml_points(:,3)-bregma(3))*atlas_resolution;
+
+% roi_location_curr = [ap dv ml];
+
+% initialize array of region annotations
+roi_annotation_curr = cell(size(apdvml_points,1),3);
+
+% loop through every point to get ROI locations and region annotations
+tf_rows = true(size(apdvml_points,1),1);
+for point = 1:size(apdvml_points,1)
+
+    % find the annotation, name, and acronym of the current ROI pixel
+    depth = ceil(apdvml_points(point,2));
+    if depth >= 1
+
+        ann = av(ceil(apdvml_points(point,1)), ...
+            depth, ... %NOTE this can take the value of 0 and cause an error (must be >= 1)
+            ceil(apdvml_points(point,3)));
+        name = st.safe_name{ann};
+        acr = st.acronym{ann};
+
+        roi_annotation_curr{point,1} = ann;
+        roi_annotation_curr{point,2} = name;
+        roi_annotation_curr{point,3} = acr;
+
+    else
+        % ignore this point, too dorsal
+        roi_annotation_curr{point,1} = NaN;
+        roi_annotation_curr{point,2} = '';
+        roi_annotation_curr{point,3} = '';
+
+    end
+
+end
+
+Tapdvml = [table(ap, dv, accf2pxs_mm(dv), ml, 'VariableNames',{'ap_mm','dv_mm', 'dv_mm_paxinos', 'ml_mm'}), ...
+    cell2table(roi_annotation_curr, 'VariableNames', {'annotation', 'name', 'acronym'})];
+
+end