update first_pass_map with flipped cerebellum

Author: nsteinme

needles/Run_Needles.m

@@ -1,7 +1,7 @@
-function Run_Needles
+function h = Run_Needles
 
 cwd = fileparts(mfilename('fullpath'));
 addpath(genpath(strrep( cwd, 'needles', 'ibllib')))
 addpath(genpath(cwd))
 
-Needles
+h = Needles;

needles/insert_electrodes_new_1.m

@@ -329,9 +329,190 @@
 
 end
 
+%% version 6: switching cerebellum/medulla to right hemi
+e.removeAll();
+
+useExclusions = true;
+
+tilt1 = 10; 
+tilt2 = 15;
+spacing = 0.5; % mm
+
+angle = 90+tilt1; dep = 14e-3; minLR = 0.8;
+% apOffset = spacing/2; nspx = 6; nspy = 8;
+apOffset = 0; nspx = 4; nspy = 6;
+
+exclSites = [...
+    2.5 -1; ...
+    2.5 minLR+spacing*0; ...
+    2.5 minLR+spacing*1; ... 
+    2 -1; ...
+    2 minLR+spacing*0; ...
+    2 minLR+spacing*1; ... 
+    2 minLR+spacing*2; ... 
+    1.5 minLR+spacing*1; ... 
+    1.5 minLR+spacing*2; ... 
+    -4 minLR+spacing*3; ...
+    -4 minLR+spacing*4; ...    
+    -4.5 minLR+spacing*2; ... 
+%     -5 minLR+spacing*0; ...
+%     -5 minLR+spacing*1; ... 
+    -5.5 minLR+spacing*1; ...
+    -5.5 minLR+spacing*4; ...
+%     -5.5 minLR+spacing*5; ...
+    -6 minLR+spacing*2; ...
+    -6 minLR+spacing*5; ...
+    -6.5 minLR+spacing*2; ...
+    -6.5 minLR+spacing*3; ...
+    -7 minLR+spacing*2; ...
+    -7.5 minLR+spacing*1; ...
+    ];
+
+xPos = -5.5:spacing:2.5;
+yPos = [-1.0 -0.5 minLR:spacing:4];
+for xidx = 1:numel(xPos)
+    xx = xPos(xidx); 
+    for yidx = 1:numel(yPos)
+        yy = yPos(yidx);
+
+        if useExclusions && ismember([xx yy], exclSites, 'rows')
+            continue; 
+        end
+        
+        if yy<0
+            useAngle = 90+17;
+            useYY = yy;
+        else
+            useAngle = angle;
+            useYY = yy; 
+        end
+        e.add_probe_by_start_angles(...
+            [dvTopForAPslice(ba, xx*1e-3) -useYY*1e-3 (xx+apOffset)*1e-3], ...
+            [90 useAngle], dep, ba, xidx-16, -(yidx-2));
+    end
+end
+
+exclSites = [0 0];
+
+xPos = -7.5:spacing:-5.6;
+yPos = [minLR:spacing:4];
+for xidx = 1:numel(xPos)
+    xx = xPos(xidx); 
+    for yidx = 1:numel(yPos)
+        yy = yPos(yidx);
+
+        if useExclusions && ismember([xx yy], exclSites, 'rows')
+            continue; 
+        end
+                
+        useAngle = angle;
+        useYY = yy;
+        
+        e.add_probe_by_start_angles(...
+            [dvTopForAPslice(ba, xx*1e-3) useYY*1e-3 (xx+apOffset)*1e-3], ...
+            [90 useAngle], dep, ba, xidx-16, -(yidx-2));
+    end
+end
+
+n1 = e.n;
+
+
+angle = 90-tilt2; dep = 4e-3; minLR = 0.8;
+
+exclSites = [...
+    1 minLR+spacing*5; ...
+    1 minLR+spacing*6; ...
+    1 minLR+spacing*7; ...
+    0.5 minLR+spacing*6; ...
+    0.5 minLR+spacing*7; ...
+    0.5 minLR+spacing*8; ...
+    0 minLR+spacing*6; ...
+    0 minLR+spacing*7; ...
+    0 minLR+spacing*8; ...
+    -0.5 minLR+spacing*6; ...
+    -0.5 minLR+spacing*7; ...
+    -0.5 minLR+spacing*8; ...
+    -1 minLR+spacing*7; ...
+    -1 minLR+spacing*8; ...
+    -1.5 minLR+spacing*7; ...
+    -1.5 minLR+spacing*8; ...
+    -2 minLR+spacing*7; ...
+    -2 minLR+spacing*8; ...
+    -2.5 minLR+spacing*7; ...
+    -2.5 minLR+spacing*8; ...
+    -3 minLR+spacing*7; ...
+    -3 minLR+spacing*8; ...
+    -3.5 minLR+spacing*7; ...
+    -3.5 minLR+spacing*8; ...
+    -4.5 minLR+spacing*5; ...
+    -4.5 minLR+spacing*6; ...
+    -4.5 minLR+spacing*7; ...
+    -5 minLR+spacing*6; ...    
+    -5.5 minLR+spacing*6; ...    
+    ];
+xPos = -5.5:spacing:3;
+yPos = minLR:spacing:5.0;
+for xidx = 1:numel(xPos)
+    xx = xPos(xidx); 
+    for yidx = 1:numel(yPos)
+        yy = yPos(yidx);
+
+        if useExclusions && ismember([xx yy], exclSites, 'rows')
+            continue; 
+        end
+        
+        e.add_probe_by_start_angles(...
+            [dvTopForAPslice(ba, xx*1e-3) -yy*1e-3 xx*1e-3], ...
+            [90 angle], dep, ba, xidx-16, -yidx);        
+    end
+end
+
+exclSites = [0 0];
+xPos = -7.5:spacing:-5.6;
+yPos = 0.3:spacing:5.0;
+for xidx = 1:numel(xPos)
+    xx = xPos(xidx); 
+    for yidx = 1:numel(yPos)
+        yy = yPos(yidx);
+
+        if useExclusions && ismember([xx yy], exclSites, 'rows')
+            continue; 
+        end
+        
+        e.add_probe_by_start_angles(...
+            [dvTopForAPslice(ba, xx*1e-3) yy*1e-3 xx*1e-3], ...
+            [90 angle], dep, ba, xidx-16, -yidx);        
+    end
+end
+
+fprintf('n penetrations = %d (%d and %d)\n', e.n, n1, e.n-n1);
+
+nPerMouse = 10; 
+% N = (e.n-3)*2 + 3*5 + (M*2/3-5)
+% M = N/nPerMouse
+% so - 
+% N - N/nPerMouse*2/3 = 2*e.n + 4
+N = (2*e.n + 4) / (1-2/nPerMouse/3);
+M = N/nPerMouse; 
+
+fprintf(1, 'total N = %d, M = %d (at %d pens per mouse)\n', round(N), round(M), nPerMouse);
+
+% plot1: by AP position
+f = figure; f.Color = 'w'; f.Position = [17          42        1239         656];
+
+uAP = unique(e.dvmlap_entry(:,3));
+for a = 1:numel(uAP)
+    ax = subtightplot(nspx,nspy,a, 0.01, 0.01, 0.01);
+    h = e.plot_probes_at_slice(ba, ax, uAP(a));
+    set(h, 'LineWidth', 2.0);
+    title(sprintf('%.2f', uAP(a)*1e3))
+    drawnow;    
+    
+end
+
 %% gif to compare the previous full map to the cut-down one
 
-filename = 'mapCompare.gif';
+filename = 'mapCompare2.gif';
 
 frame = getframe(fCut);
 im = frame2im(frame);
@@ -426,7 +607,7 @@
 
 %% plot: recording locations top down
 
-% av = readNPY('/Users/nick/Documents/allenCCFdata/annotation_volume_10um_by_index.npy');
+av = readNPY('/Users/nick/Documents/allenCCFdata/annotation_volume_10um_by_index.npy');
 szAV = [1320 800 1140];
 mlCoords = (1:szAV(3))*10+ba.brain_coor.x0*1e6; 
 apCoords = (1:szAV(1))*10*1.087-max(ba.brain_coor.yscale)*1e6;