resolving merge issues

CellReg/demo.m

@@ -29,12 +29,11 @@
 
 %% Setting paths for the cell registration procedure:
 
-% we need to find the path up-two levels
-[fileroot,~,~] = fileparts(mfilename('fullpath'));
-[fileroot,~,~] = fileparts(fileroot);
+% Defining the data directory:
+data_path='D:\dev\Cell registration\CellReg';
 
 % Defining the results_directory and creating the figures_directory:
-results_directory= fullfile(fileroot,'SampleData', 'Results') ;
+results_directory=fullfile(data_path,'SampleData','Results') ;
 
 figures_directory=fullfile(results_directory,'Figures');
 if exist(figures_directory,'dir')~=7
@@ -43,11 +42,11 @@
 
 figures_visibility='on'; % either 'on' or 'off' (in any case figures are saved)
 
-% define path of sample data
+% define file names of sample data:
 number_of_sessions=5;
 file_names=cell(1,number_of_sessions);
-for it = 1:number_of_sessions
-    file_names{it} = fullfile(fileroot, 'SampleData',sprintf('spatial_footprints_0%1i.mat',it));
+for file_index=1:number_of_sessions
+    file_names{file_index}=fullfile(data_path,'SampleData',sprintf('spatial_footprints_0%1i.mat',file_index));
 end
 
 %% Stage 1 - Loading the spatial footprints of cellular activity:

CellReg_setup.m

@@ -1,4 +1,5 @@
 CellReg_directory=fileparts(which('CellReg_setup.m'));
 addpath(genpath(fullfile(CellReg_directory,'CellReg')));
 addpath(genpath(fullfile(CellReg_directory,'GUI')));
+addpath(genpath(fullfile(CellReg_directory,'Helper')));
 savepath();

Helper/format_conversion_Suite2p_CNMF_e.m

@@ -0,0 +1,46 @@
+%% Converting the outputs from CNMF-e or Suite2p to the required input format for CellReg
+
+input_format='Suite2p'; % could be either 'CNMF-e' or 'Suite2p'
+
+%% Choosing the files for conversion:
+[file_names,files_path]=uigetfile('*.mat','MultiSelect','on',...
+    'Choose the spatial footprints from all the sessions: ' );
+
+if iscell(file_names)
+    number_of_sessions=size(file_names,2);
+else
+    number_of_sessions=1;
+end
+for n=1:number_of_sessions
+    if iscell(file_names)
+        this_session_data=load([files_path file_names{n}]);
+    else
+        this_session_data=load([files_path file_names]);
+    end
+    if strcmp(input_format,'Suite2p')
+        this_session_x_size=this_session_data.ops.Lx+1;
+        this_session_y_size=this_session_data.ops.Ly+1;
+        this_session_num_cells=size(this_session_data.stat,2);
+        this_session_converted_footprints=zeros(this_session_num_cells,this_session_y_size,this_session_x_size);
+        for k=1:this_session_num_cells
+            for l=1:length(this_session_data.stat{k}.ypix)
+                this_session_converted_footprints(k,this_session_data.stat{k}.ypix(l)+1,this_session_data.stat{k}.xpix(l)+1)=this_session_data.stat{k}.lam(l);
+            end
+        end
+
+    elseif strcmp(input_format','CNMF-e')
+        this_session_y_size=this_session_data.neuron.options.d1;
+        this_session_x_size=this_session_data.neuron.options.d2;
+        this_session_num_cells=size(this_session_data.neuron.A,2);
+        this_session_converted_footprints=zeros(this_session_num_cells,this_session_y_size,this_session_x_size);
+        for k=1:this_session_num_cells
+            this_session_converted_footprints(k,:,:)=reshape(this_session_data.neuron.A(:,k),this_session_y_size,this_session_x_size);
+        end
+    end
+    if iscell(file_names)
+        save([files_path 'converted_' file_names{n}],'this_session_converted_footprints','-v7.3')
+    else
+        save([files_path 'converted_' file_names],'this_session_converted_footprints','-v7.3')
+    end
+end
+

Helper/format_conversion_inscopix.m

@@ -0,0 +1,29 @@
+%% Converting the Inscopix .tif cell spatial footprints to input format for CellReg
+
+[files_path]=uigetdir('Choose the location of the footprints from one session: ' );
+file_names = dir(fullfile(files_path, '**', '*_CNMFe_CellSet_C*'));
+%
+this_session_num_cells = length(file_names);
+
+% get size of footprints first
+fname = file_names(1);
+fname = fullfile(fname.folder, fname.name);
+footprint = read(Tiff(fname,'r'));  
+[~,folder_name] = fileparts(files_path);
+%
+this_session_converted_footprints=zeros(this_session_num_cells,size(footprint, 1), size(footprint, 2));
+
+%
+for n=1:this_session_num_cells
+
+    fname = file_names(n);
+    fname = fullfile(fname.folder, fname.name);
+
+    %
+    footprint = read(Tiff(fname,'r'));    
+    this_session_converted_footprints(n,:,:)= footprint;
+
+end
+fname_out = fullfile(file_names(1).folder, [folder_name, '_converted.mat']);
+save(fname_out,'this_session_converted_footprints','-v7.3')
+

Helper/s2pToCellReg.m

@@ -47,3 +47,5 @@
 
 
 end
+
+

README.md

@@ -5,12 +5,12 @@ in Ca2+ imaging data. The package includes a GUI that supports the entire regist
 For more information contact [email protected] or join our [slack channel](https://cellreg.slack.com).
 
 ## Setting up the repository
-We encourage the use of official versions (e.g., v1.4.5) for easier debugging processes. Switch to the releases tab on GitHub and checkout the latest version.
+We encourage the use of official versions (e.g., v1.4.9) for easier debugging processes. Switch to the releases tab on GitHub and checkout the latest version.
 
 1. Cloning:
 `git clone https://github.com/zivlab/CellReg.git`
 2. Checkout version:
-`git checkout v<major>.<minor>.<bugfix> (e.g., v1.4.5)`
+`git checkout v<major>.<minor>.<bugfix> (e.g., v1.4.9)`
 3. Run `setup.m`
 
 ## Usage and documentation