bug fixes to 3D pipeline

@iss/extract_and_filter.m

@@ -102,7 +102,7 @@
             end
 
             if (min(size(o.EmptyTiles))==1 && min(o.EmptyTiles)~=0) || ...
-                    (min(size(o.EmptyTiles)==[MaxY, MaxX]) && min(o.EmptyTiles(:))==0 && ...
+                    (min(size(o.EmptyTiles)==[o.MaxY, o.MaxX]) && min(o.EmptyTiles(:))==0 && ...
                     max(o.EmptyTiles(:)==1))
                 UsedEmptyTiles = true;
                 if min(o.EmptyTiles(:))==0
@@ -113,7 +113,7 @@
         end
 
         %Tile index in nd2 file different to index in o.EmptyTiles
-        t_save_value = sub2ind([MaxY,MaxX],o.TilePosYX(:,1),o.TilePosYX(:,2));
+        t_save_value = sub2ind([o.MaxY,o.MaxX],o.TilePosYX(:,1),o.TilePosYX(:,2));
 
         o.TilePosYXC = zeros(nSerieswPos*nChannels,3);
 

@iss/extract_and_filter_NoGPU.m

@@ -117,7 +117,7 @@
             %     SE = h2D.*hzdirection;
 
             if (min(size(o.EmptyTiles))==1 && min(o.EmptyTiles)~=0) || ...
-                    (min(size(o.EmptyTiles)==[MaxY, MaxX]) && min(o.EmptyTiles(:))==0 && ...
+                    (min(size(o.EmptyTiles)==[o.MaxY, o.MaxX]) && min(o.EmptyTiles(:))==0 && ...
                     max(o.EmptyTiles(:)==1))
                 UsedEmptyTiles = true;
                 if min(o.EmptyTiles(:))==0
@@ -129,7 +129,7 @@
         end
 
         %Tile index in nd2 file different to index in o.EmptyTiles
-        t_save_value = sub2ind([MaxY,MaxX],o.TilePosYX(:,1),o.TilePosYX(:,2));
+        t_save_value = sub2ind([o.MaxY,o.MaxX],o.TilePosYX(:,1),o.TilePosYX(:,2));
 
         %Set top hat structuring elements
         if strcmpi(o.DapiR,'auto')

@iss/get_TilePos.m

@@ -32,6 +32,8 @@
 X = uniqueX(diff([0;uniqueX])==1 & uniqueX<=nTiles);
 MaxY = max(Y);
 MaxX = max(X);
+o.MaxX = MaxX;
+o.MaxY = MaxY;
 
 %Sometimes get Nan, if only one Nan, then check if all tiles 
 %arranged along only one direction i.e. Nan should be 1.

@iss/iss.m

@@ -504,12 +504,21 @@
         % r. To get the global coordinate of a point, add this to the local
         % coordinate within the tile (counting from 1)
         TileOrigin;
-        
+
         % TileInitialPosXY(t,:): coordinate of tile t in integers. This is
         % the derived coordinates, before using the fact we know the answer
         % to get TilePosYXC.
         TileInitialPosYX;
 
+        % TilePosYX is the updated version of TileInitialPosYX, after being
+        % modified by the get_TilePos function.
+        TilePosYX;
+
+        % Temporary variables generated as a part of the get_TilePos
+        % function which are needed outside that function.
+        MaxX;
+        MaxY;
+
         %RawLocalYXZ{t} stores the YXZ coordinates of spots found in the
         %anchor round of tile t
         RawLocalYXZ;

README.md

@@ -4,3 +4,8 @@ The README of the master branch gives instructions of how to run the pipeline an
 * The figure number of ```o.plot``` is now 93454, so when calling ```iss_view_prob``` or ```iss_view_codes```, [the figure number will need to be changed to this](https://github.com/jduffield65/iss/blob/11c185d41534e46a4662a6089c50cb8fddb4b89f/bridge_process_template.m#L144-L145).
 * The ```o.plot``` figure now has a scrollbar which allows you to see how the genes are distributed at each z coordinate. To concatenate genes from other planes onto a single plane, use [```o.PlotZThick```](https://github.com/jduffield65/iss/blob/11c185d41534e46a4662a6089c50cb8fddb4b89f/bridge_process_template.m#L134). This is defined such that all genes with z coordinate within ```+/-o.PlotZThick``` of the current z coordinate (chosen by the scrollbar) are shown. After changing this, ```iss_change_plot(o)``` needs to be run for it to take effect.
 * Apart from these, there are of course many instances when 2D coordinates/shifts/transforms are converted into 3D.
+
+# System requirements
+
+- Matlab signal processing toolbox
+- Matlab image processing toolbox

bridge_process_template.m

@@ -7,7 +7,7 @@
 %CHECK BEFORE EACH RUN
 o = iss;
 o.ReferenceRound = 8;           %Round that contains Dapi image (Starting from 1).
-o.AnchorChannel =  ;            %Channel that has most spots in o.AnchorRound (Starting from 1).
+o.AnchorChannel = 5 ;            %Channel that has most spots in o.AnchorRound (Starting from 1).
 o.DapiChannel = 1;              %Channel in o.AnchorRound that contains Dapi images (Starting from 1).
 o.InitialShiftChannel = o.AnchorChannel;      %Channel to use to find initial shifts between rounds (Starting from 1).
 o.ExtractScaleChannel = o.AnchorChannel;	  %Channel which is used to get scaling for imaging rounds (Starting from 1).
@@ -17,27 +17,27 @@
 
 %% File Names
 %CHECK BEFORE EACH RUN
-o.InputDirectory = '...\Experiment1\raw_data';     %Folder path of raw data
+o.InputDirectory = '\\128.40.224.65\Subjects\FR187\ISS\seq\FR178 b2a3 b2a5\B2A3\raw_data';     %Folder path of raw data
 
 %FileBase{r} is the file name of the raw data of round r in o.InputDirectory
 o.nBP = 7;              %Number of Channels
 o.nRounds = 7;          %Number of Imaging Rounds
 o.nExtraRounds = 1;     %Treat Anchor channel as extra round
 o.FileBase = cell(o.nRounds+o.nExtraRounds,1);
-o.FileBase{1} = 'round0';
-o.FileBase{2} = 'round1';
-o.FileBase{3} = 'round2';
-o.FileBase{4} = 'round3';
-o.FileBase{5} = 'round4';
-o.FileBase{6} = 'round5';
-o.FileBase{7} = 'round6';
-o.FileBase{8} = 'anchor';    %Make sure the last round is the anchor
-
-o.TileDirectory = '...\Experiment1\tiles'; 
-o.OutputDirectory = '...\Experiment1\output';  
+o.FileBase{1} = 'FR178_b2a3_R0';
+o.FileBase{2} = 'FR178_b2a3_R1';
+o.FileBase{3} = 'FR178_b2a3_R2';
+o.FileBase{4} = 'FR178_b2a3_R3';
+o.FileBase{5} = 'FR178_b2a3_R4';
+o.FileBase{6} = 'FR178_b2a3_R5';
+o.FileBase{7} = 'FR178_b2a3_R6';
+o.FileBase{8} = 'FR178_b2a3_R7';    %Make sure the last round is the anchor
+
+o.TileDirectory = '\\128.40.224.65\Subjects\FR187\ISS\seq\FR178 b2a3 b2a5\B2A3\tiles'; 
+o.OutputDirectory = '\\128.40.224.65\Subjects\FR187\ISS\seq\FR178 b2a3 b2a5\B2A3\output';  
 %Codebook is a text file containing 2 columns - 1st is the gene name. 2nd is
 %the code, length o.nRounds and containing numbers in the range from 0 to o.nBP-1.
-o.CodeFile = '\\zserver\Data\ISS\codebook_73gene_6channels_2col.txt';
+o.CodeFile = 'C:\Users\Experiment\Documents\GitHub\73g_codebook';
 
 %% Logging
 if o.LogToFile