added neuropil coef in GUI

shinkira · Feb 18, 2017 · 385ec15 · 385ec15
1 parent 7d1a7f0
commit 385ec15
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Showing 4 changed files with 30 additions and 9 deletions.
diff --git a/SpikeDetection/run_deconvolution3.m b/SpikeDetection/run_deconvolution3.m
@@ -31,7 +31,12 @@
 [NT, NN] = size(Ff);
 
 ops.fs            = getOr(ops, 'fs', ops.imageRate/ops.nplanes);
-[coefNeu, inomax] = my_ica(Ff, Fneu, ops.fs, coefDefault);
+
+if ~isfield(stat, 'neuropilCoefficient')
+    [coefNeu, inomax] = my_ica(Ff, Fneu, ops.fs, coefDefault);
+else
+   coefNeu = [stat.neuropilCoefficient]; 
+end
 
 Ff = Ff - bsxfun(@times, Fneu, coefNeu(:)');
 

diff --git a/gui2P/new_main.m b/gui2P/new_main.m
@@ -494,6 +494,7 @@ function pushbutton98_Callback(hObject, eventdata, h)
 
 function pushbutton99_Callback(hObject, eventdata, h)
 hval = max(0, [h.dat.stat.cmpct]-1);
+% hval = max(0, [h.dat.stat.aspect_ratio]-1);
 h.dat.cl.rands   = .1 + .8 * min(1, .5 * hval/mean(hval));
 h.dat.cl.rands_orig = h.dat.cl.rands;
 redraw_figure(h);

diff --git a/gui2P/redraw_fluorescence.m b/gui2P/redraw_fluorescence.m
@@ -14,8 +14,13 @@ function redraw_fluorescence(h)
 axis tight
 hold on
 
+coefNeu = 0.7;
+if isfield(h.dat.stat, 'neuropilCoefficient')
+    coefNeu = h.dat.stat(ichosen).neuropilCoefficient;
+end
+
 if isfield(h.dat, 'FcellNeu')
-    plot(my_conv_local(medfilt1(double(Fneu), 3), 3))
+    plot(coefNeu * my_conv_local(medfilt1(double(Fneu), 3), 3))
 end
 
 box off

diff --git a/signalExtraction/extractSignals.m b/signalExtraction/extractSignals.m
@@ -107,16 +107,25 @@
 indNoNaN    = find(~ops.badframes);
 ix          = cumsum(~ops.badframes) + 1;
 ix          = ix(ops.badframes);
-ix(ix>numel(indNoNaN)) = numel(indNoNaN);
+ix(ix>numel(indNoNaN))  = numel(indNoNaN);
 
-F(:, ops.badframes)     = F(:, indNoNaN(ix));
+   F(:, ops.badframes)  = F(:,    indNoNaN(ix));
 Fneu(:, ops.badframes)  = Fneu(:, indNoNaN(ix));
 
-dF = F - Fneu;
-sd = std(dF, [], 2);
+
+% figure out the ICA coefficients here <--- FIX THIS
+ops.fs           = getOr(ops, 'fs', ops.imageRate/ops.nplanes);
+%
+[coefNeu, inomax]   = my_ica(F', Fneu', ops.fs, 0.7);
+dF                  = F - bsxfun(@times, Fneu, coefNeu(:));
+
+% dF          = F - Fneu;
+
+sd           = std(dF, [], 2);
+sdN          = std(Fneu, [], 2);
 
 sk(:, 1) = skewness(dF, [], 2);
-sk(:, 2) = sd/mean(sd); 
+sk(:, 2) = sd./sdN; 
 sk(:, 3) = (max(dF, [], 2)-median(dF, 2))./sd;
 sk(:, 4) = (prctile(dF, 95, 2)-median(dF, 2))./sd;
 
@@ -127,10 +136,11 @@
     stat(j).maxMinusMed      = sk(j,3);
     stat(j).top5pcMinusMed   = sk(j,4);
     stat(j).blockstarts      = [0 cumsum(ops.Nframes)];
-    stat(j).iplane           = ops.iplane;
+    stat(j).iplane                 = ops.iplane;
+    stat(j).neuropilCoefficient    = coefNeu(j); 
 end
 
-%%
+%
 csumNframes = [0 cumsum(ops.Nframes)];
 Fcell       = cell(1, length(ops.Nframes));
 FcellNeu    = cell(1, length(ops.Nframes));