From 36ef7ead1f5e9aaf1bf6107f4b2d0146405a4c3a Mon Sep 17 00:00:00 2001
From: Florian Vollrath <florian.vollrath@brain.mpg.de>
Date: Wed, 7 Sep 2016 14:46:51 +0200
Subject: [PATCH] added an output of merged cell_signals and some information
 to select PCAs manually

---
 alternativePlot.m |  9 +++++++--
 main.m            | 11 ++++++-----
 2 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/alternativePlot.m b/alternativePlot.m
index 4fe762a..86578a3 100644
--- a/alternativePlot.m
+++ b/alternativePlot.m
@@ -1,4 +1,4 @@
-function alternativePlot(ica_segments, cluster, cell_sig, subPlotCols, sortedIdx, data_r)
+function cell_sig_merged = alternativePlot(ica_segments, cluster, cell_sig, subPlotCols, sortedIdx, data_r)
 cm = colormap(hsv);
 tempImage = zeros(size(ica_segments, 2), size(ica_segments, 3), 3);
 
@@ -23,7 +23,7 @@ function alternativePlot(ica_segments, cluster, cell_sig, subPlotCols, sortedIdx
 end
 %set pixels 0 which are smaller than 0, seems to happen in rare cases..
 for i = 1:3
-tempImage(:,:,i) = (tempImage(:,:,i) > 0).*tempImage(:,:,i);
+    tempImage(:,:,i) = (tempImage(:,:,i) > 0).*tempImage(:,:,i);
 end
 %scale tempImage
 % maximum = max(tempImage(:));
@@ -51,8 +51,13 @@ function alternativePlot(ica_segments, cluster, cell_sig, subPlotCols, sortedIdx
 subplot(1,2,2);
 hold on
 cell_sigPlot = cell_sig(sortedIdx,:);
+
+
+
 signal = zeros(size(cluster,2),size(cell_sig,2));
 for i = 1:size(cluster, 2)
+    cell_sig_merged{i} = cell_sig(sortedIdx,:);
+cell_sig_merged{i} = mean(cell_sig_merged{i}(cluster{i},:), 1);
     for clusterIdx = cluster{i}
         %subtract minimum value
         minimum = min(cell_sigPlot(clusterIdx,:));
diff --git a/main.m b/main.m
index 8a788e2..68810ae 100644
--- a/main.m
+++ b/main.m
@@ -34,7 +34,8 @@
 %choose PCAs, type f/b in command line to go back or forward. type two number
 %to select the range "1 ENTER 25 ENTER" would select the PCAs from 1 to 25
 [PCuse] = CellsortChoosePCs(fn_green, mixedfilters, data_g);
-
+%OR specify the PCAs to use manually:
+%PCuse = [2,3,6,13,16,17,18,19,21,22,23,25,29,30];
 %% 2b. Plot PC spectrum
 %optionally, you can display the PC spectrum..
 CellsortPlotPCspectrum(fn_green, CovEvals, PCuse, data_g)
@@ -67,8 +68,8 @@
 %plotting: 1 = yes or 0 = no.. shall a plot be shown or not?
 
 smwidth = 1;
-thresh = 2;
-arealims = [250];
+thresh = 1.5;
+arealims = [200];
 plotting = 1;
 
 [ica_segments, segmentlabel, segcentroid] = CellsortSegmentation(ica_filters, smwidth, thresh, arealims, plotting);
@@ -94,7 +95,7 @@
 %% show signal of cells (cell_sig)
 %caluclate correlation matrix for cell_sig
 [ica_segments, cluster, subPlotCols, subPlotWidth, sortedIdx] = calcCorrEff(cell_sig, ica_segments);
-alternativePlot(ica_segments, cluster, cell_sig, subPlotCols, sortedIdx, data_r);
+cell_sig_merged = alternativePlot(ica_segments, cluster, cell_sig, subPlotCols, sortedIdx, data_r);
 
 %% let user deselect and merge rois
 %merge -> change cluster ->recereate plots
@@ -117,4 +118,4 @@
 subPlotCols = size(cluster_new, 2);
 
 %redraw
-alternativePlot(ica_segments, cluster_new, cell_sig, subPlotCols, sortedIdx, data_r);
+cell_sig_merged = alternativePlot(ica_segments, cluster_new, cell_sig, subPlotCols, sortedIdx, data_r);