From abd851a6cbb0a92238fac2d26a0b9a0c13fe82e9 Mon Sep 17 00:00:00 2001
From: danielsnider <danielsnider12@gmail.com>
Date: Fri, 14 Jul 2017 16:31:36 -0400
Subject: [PATCH] Cell size analysis scaling for z-resolution

---
 .gitignore                      |  1 +
 daniel/size_analysis_3rd_set.m  | 57 +++++++++++++++++++++++++++++++++
 islet_functions/normalize0to1.m |  8 +++++
 3 files changed, 66 insertions(+)
 create mode 100644 daniel/size_analysis_3rd_set.m
 create mode 100644 islet_functions/normalize0to1.m

diff --git a/.gitignore b/.gitignore
index b2e6ee2..557a447 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,5 @@
 *.pptx
+*.asv
 *.mat
 *.lnk
 ResultTables/
diff --git a/daniel/size_analysis_3rd_set.m b/daniel/size_analysis_3rd_set.m
new file mode 100644
index 0000000..dedd05a
--- /dev/null
+++ b/daniel/size_analysis_3rd_set.m
@@ -0,0 +1,57 @@
+%load 'Z:\DanielS\old\pancreatic_islets\ResultsTable_3rdSet_3D.mat'
+%load 'Z:\DanielS\old\pancreatic_islets\ResultsTable.mat'
+% load 'Z:\DanielS\old\pancreatic_islets\ResultsTable3D.mat'
+load 'Z:\YuvalDor\mouse islet z-stacks\code\ResultTables\ResultsTable_3rdSet_3D.mat'
+unique(ResultsTable.Stack)
+
+% Store the z-resolution that each stack was imaged at
+stack_z_resolutions = containers.Map;
+stack_z_resolutions('Cont23') = 0.15; % microns
+stack_z_resolutions('Cont24') = 0.05; % microns
+stack_z_resolutions('Cont25') = 0.1; % microns
+stack_z_resolutions('Wash20') = 0.15; % microns
+stack_z_resolutions('Wash22') = 0.1; % microns
+stack_z_resolutions('Tor21') = 0.15; % microns
+stack_z_resolutions('Tor20') = 0.12; % microns
+stack_z_resolutions('Tor22') = 0.15; % microns
+max_z_resolution = max(cell2mat(stack_z_resolutions.values));
+
+% Filter out bad cells (upper and lower outliers)
+subsetTable=ResultsTable(ResultsTable.CellSize<prctile(ResultsTable.CellSize,80),:);
+
+% Scale cell sizes according to z-resolution (this does not calculate actual volume)
+stack_names = unique(subsetTable.Stack,'stable');
+for i=1:length(stack_names)
+    stack_names(i)
+    stack_size_scale_factor = max_z_resolution/stack_z_resolutions(char(stack_names(i)))
+    temp = subsetTable(strcmp(subsetTable.Stack,stack_names(i)),:);
+    subsetTable.CellSize(strcmp(subsetTable.Stack,stack_names(i))) = temp.CellSize / stack_size_scale_factor;
+end
+
+% Bar chart (per stack)
+Means = grpstats(subsetTable.CellSize,subsetTable.Stack,'mean');
+Stds = grpstats(subsetTable.CellSize,subsetTable.Stack,'std');
+Lngth = grpstats(subsetTable.CellSize,subsetTable.Stack,'numel');
+figure
+bar(Means)
+hold on
+errorbar(Means,Stds./sqrt(Lngth),'.r')
+ylabel('Cell Area (pixel count)', 'FontSize', 21);
+for i=1:length(Means)
+  text(i+0.06,Means(i)+30,int2str(Means(i)),'FontSize',20);
+end
+set(gca,'FontSize',19,'XTickLabel',unique(subsetTable.Stack,'stable'))   
+
+% Bar chart (experimental classes)
+Means = grpstats(subsetTable.CellSize,subsetTable.Experiment,'mean');
+Stds = grpstats(subsetTable.CellSize,subsetTable.Experiment,'std');
+Lngth = grpstats(subsetTable.CellSize,subsetTable.Experiment,'numel');
+figure
+bar(Means)
+hold on
+errorbar(Means,Stds./sqrt(Lngth),'.r')
+ylabel('Cell Area (pixel count)', 'FontSize', 21);
+for i=1:length(Means)
+  text(i+0.06,Means(i)+30,int2str(Means(i)),'FontSize',20);
+end
+set(gca,'FontSize',19,'XTickLabel',unique(subsetTable.Experiment,'stable'))
diff --git a/islet_functions/normalize0to1.m b/islet_functions/normalize0to1.m
new file mode 100644
index 0000000..28b5146
--- /dev/null
+++ b/islet_functions/normalize0to1.m
@@ -0,0 +1,8 @@
+function normalized = normalize0to1(mat)
+  if length(mat)==1
+    % one sample can't be normalized
+    normalized = mat;
+  else
+    normalized = (mat-min(mat(:)))./(max(mat(:))-min(mat(:)));
+  end
+end