diff --git a/main_kilosort.m b/main_kilosort.m
index 93ab5986..a13364d2 100644
--- a/main_kilosort.m
+++ b/main_kilosort.m
@@ -40,6 +40,10 @@
 % main tracking and template matching algorithm
 rez = learnAndSolve8b(rez);
 
+% OPTIONAL: remove double-counted spikes - solves issue in which individual spikes are assigned to multiple templates.
+% See issue 29: https://github.com/MouseLand/Kilosort2/issues/29
+%rez = remove_ks2_duplicate_spikes(rez);
+
 % final merges
 rez = find_merges(rez, 1);
 
diff --git a/postProcess/remove_ks2_duplicate_spikes.m b/postProcess/remove_ks2_duplicate_spikes.m
new file mode 100644
index 00000000..7b04661a
--- /dev/null
+++ b/postProcess/remove_ks2_duplicate_spikes.m
@@ -0,0 +1,134 @@
+% REMOVE_KS2_DUPLICATE_SPIKES2 Double-counted spikes are hard to avoid with
+% Kilosort's template matching algorithm since the overall fit can be
+% improved by having multiple templates jointly account for a single variable waveform.
+% 
+% This function takes the kilosort2 output rez and identifies pair of
+% spikes that are close together in time and space. The temporal threshold
+% is give by the parameter OVERLAP_S which is 0.5ms by default and
+% the spatial threshold (applied to the template primary sites) is given by
+% CHANNEL_SEPARATION_UM and is 100 by default.
+%
+% From these spike pairs, it identifies the pair with the larger template as
+% being the "main" or "reference" cluster and the duplicate spikes from the
+% other cluster are removed.
+%
+% All spike pairs are considered, not just those from CCG-contaminated
+% pairs, as in REMOVE_KS2_DUPLICATE_SPIKES2.
+%
+% Adrian Bondy, 2020
+%
+%=INPUT
+%
+%   rez structure
+%
+%=OPTIONAL INPUT, NAME-VALUE PAIRS
+%
+%   overlap_s
+%       the time interval, in second, within which a sequence of spikes are
+%       vetted for duplicates.
+%
+%   channel_separation_um
+%       When the primay channels of two spikes are within this distance, in
+%       microns, then the two spikes are vetted for duplicate.
+%
+%=EXAMPLE
+%
+%   >> rez = remove_ks2_duplicate_spikes(rez)
+function rez = remove_ks2_duplicate_spikes(rez, varargin)
+    input_parser = inputParser;
+    addParameter(input_parser, 'overlap_s', 5e-4, @(x) (isnumeric(x))) % the temporal window within which pairs of spikes will be considered duplicates (if they are also within the spatial window)
+    addParameter(input_parser, 'channel_separation_um', 100, @(x) (ischar(x))) % the spatial window within which pairs of spikes will be considered duplicates (if they are also within the temporal window)
+    parse(input_parser, varargin{:});
+    P = input_parser.Results;
+
+    spike_times = uint64(rez.st3(:,1));
+    spike_templates = uint32(rez.st3(:,2));
+
+    rez.U=gather(rez.U);
+    rez.W = gather(rez.W);
+    templates = zeros(rez.ops.Nchan, size(rez.W,1), size(rez.W,2), 'single');
+    for iNN = 1:size(templates,3)
+       templates(:,:,iNN) = squeeze(rez.U(:,iNN,:)) * squeeze(rez.W(:,iNN,:))';
+    end
+    templates = permute(templates, [3 2 1]); % now it's nTemplates x nSamples x nChannels
+    n_spikes=numel(spike_times);        
+    %% Make sure that the spike times are sorted
+    if ~issorted(spike_times)
+        [spike_times, spike_idx] = sort(spike_times);
+        spike_templates = spike_templates(spike_idx);
+    else
+        spike_idx=(1:n_spikes)';
+    end
+    %% deal with cluster 0
+    if any(spike_templates==0)
+        error('Currently this function can''t deal with existence of cluster 0. Should be OK since it ought to be run first in the post-processing.');
+    end
+    %% Determine the channel where each spike had that largest amplitude (i.e., the primary) and determine the template amplitude of each cluster
+    whiteningMatrix = rez.Wrot/rez.ops.scaleproc;
+    whiteningMatrixInv = whiteningMatrix^-1;
+
+    % here we compute the amplitude of every template...
+    % unwhiten all the templates
+    tempsUnW = zeros(size(templates));
+    for t = 1:size(templates,1)
+        tempsUnW(t,:,:) = squeeze(templates(t,:,:))*whiteningMatrixInv;
+    end
+
+    % The amplitude on each channel is the positive peak minus the negative
+    tempChanAmps = squeeze(max(tempsUnW,[],2))-squeeze(min(tempsUnW,[],2));
+
+    % The template amplitude is the amplitude of its largest channel
+    [tempAmpsUnscaled,template_primary] = max(tempChanAmps,[],2);
+    %without undoing the whitening
+    %template_amplitude = squeeze(max(templates, [], 2) - min(templates, [], 2));
+    %[~, template_primary] = max(template_amplitude, [], 2); 
+
+    template_primary = cast(template_primary, class(spike_templates));
+    spike_primary = template_primary(spike_templates);
+
+    %% Number of samples in the overlap
+    n_samples_overlap = round(P.overlap_s * rez.ops.fs);
+    n_samples_overlap = cast(n_samples_overlap, class(spike_times));
+    %% Distance between each channel
+    chan_dist = ((rez.xcoords - rez.xcoords').^2 + (rez.ycoords - rez.ycoords').^2).^0.5;
+    n_spikes=numel(spike_times);
+    remove_idx = [];
+    reference_idx = [];
+    % check pairs of spikes in the time-ordered list for being close together in space and time. 
+    % Check pairs that are separated by N other spikes,
+    % starting with N=0. Increasing N until there are no spikes within the temporal overlap window. 
+    % This means only ever computing a vector operation (i.e. diff(spike_times))
+    % rather than a matrix one (i.e. spike_times - spike_times').
+    diff_order=0;
+    while 1==1
+        diff_order=diff_order+1;
+        fprintf('Now comparing spikes separated by %g other spikes.\n',diff_order-1);
+        isis=spike_times(1+diff_order:end) - spike_times(1:end-diff_order);
+        simultaneous = isis<n_samples_overlap;
+        if any(isis<0)
+            error('ISIs less than zero? Something is wrong because spike times should be sorted.');
+        end
+        if ~any(simultaneous)
+            fprintf('No remaining simultaneous spikes.\n');
+            break
+        end
+        nearby = chan_dist(sub2ind(size(chan_dist),spike_primary(1:end-diff_order),spike_primary(1+diff_order:end)))<P.channel_separation_um;
+        first_duplicate = find(simultaneous & nearby); % indexes the first (earliest in time) member of the pair
+        n_duplicates = length(first_duplicate);
+        if ~isempty(first_duplicate)
+            fprintf('On iteration %g, %g duplicate spike pairs were identified.\n',diff_order,n_duplicates);
+            amps_to_compare=tempAmpsUnscaled(spike_templates([first_duplicate first_duplicate(:)+diff_order]));
+            if length(first_duplicate)==1
+                amps_to_compare = amps_to_compare(:)'; % special case requiring a dimension change
+            end
+            first_is_bigger =  diff(amps_to_compare,[],2)<=0;
+            remove_idx = [remove_idx ; spike_idx([first_duplicate(~first_is_bigger);(first_duplicate(first_is_bigger)+diff_order)])];
+            reference_idx = [reference_idx ; spike_idx([(first_duplicate(~first_is_bigger)+diff_order);first_duplicate(first_is_bigger)])];
+        end
+    end
+    [remove_idx,idx] = unique(remove_idx);
+    reference_idx = reference_idx(idx);    
+    logical_remove_idx = ismember((1:n_spikes)',remove_idx);
+    rez = remove_spikes(rez,logical_remove_idx,'duplicate','reference_time',spike_times(reference_idx),...
+        'reference_cluster',spike_templates(reference_idx));
+end
\ No newline at end of file
diff --git a/postProcess/remove_spikes.m b/postProcess/remove_spikes.m
new file mode 100644
index 00000000..18afc5a1
--- /dev/null
+++ b/postProcess/remove_spikes.m
@@ -0,0 +1,52 @@
+function rez = remove_spikes(rez,remove_idx,label,varargin)
+    if ~islogical(remove_idx)
+        error('remove_idx must be logical.');
+    end
+    if ~any(remove_idx)
+        return
+    end
+    fprintf('Removing %g spikes from rez structure.\n',sum(remove_idx));            
+    if ~isfield(rez,'removed')
+        [rez.removed.cProj,rez.removed.cProjPC,rez.removed.st2,rez.removed.st3] = deal([]);
+        rez.removed.label={};
+    end
+    L2 = size(rez.removed.cProj,1);
+    if ~isempty(rez.cProj)
+        rez.removed.cProj = cat(1,rez.removed.cProj,rez.cProj(remove_idx,:));
+        rez.removed.cProjPC = cat(1,rez.removed.cProjPC,rez.cProjPC(remove_idx,:,:));
+    end
+    rez.removed.st3 = cat(1,rez.removed.st3,rez.st3(remove_idx,:));
+    rez.removed.st2 = cat(1,rez.removed.st2,rez.st2(remove_idx,:));
+
+    rez.removed.label = cat(1,rez.removed.label,repmat({label},sum(remove_idx),1));
+    k=0;
+    while k<length(varargin)
+        k=k+1;
+        if ~isfield(rez.removed,varargin{k}) || size(rez.removed.(varargin{k}),1)<L2
+            if isfield(rez.removed,varargin{k})
+                L = size(rez.removed.(varargin{k}),1);
+            else
+                L=0;
+            end
+            if ischar(varargin{k+1})
+                fill='';
+                rez.removed.(varargin{k}){L+1:size(rez.removed.cProj,1),1} = fill;
+            elseif isnumeric(varargin{k+1})
+                fill=NaN;
+                rez.removed.(varargin{k})(L+1:L2,1) = fill;
+            end
+        end   
+        if size(varargin{k+1},1)~=sum(remove_idx)
+            error('optional arg in incorrect number of rows.');
+        end
+        rez.removed.(varargin{k}) = cat(1,rez.removed.(varargin{k}),varargin{k+1});
+        k=k+1;
+    end
+    
+    if ~isempty(rez.cProj)
+        rez.cProj = rez.cProj(~remove_idx,:);
+        rez.cProjPC = rez.cProjPC(~remove_idx,:,:);
+    end
+    rez.st3 = rez.st3(~remove_idx,:);
+    rez.st2 = rez.st2(~remove_idx,:);
+end
\ No newline at end of file
diff --git a/postProcess/set_cutoff.m b/postProcess/set_cutoff.m
index 6a08ed1c..e9e41a4f 100644
--- a/postProcess/set_cutoff.m
+++ b/postProcess/set_cutoff.m
@@ -66,10 +66,5 @@
 % we sometimes get NaNs, why? replace with full contamination
 rez.est_contam_rate(isnan(rez.est_contam_rate)) = 1;
 
-% remove spikes assigned to the 0 cluster
-ix = rez.st3(:,2)==0;
-rez.st3(ix, :) = [];
-if ~isempty(rez.cProj)
-    rez.cProj(ix, :) = []; % remove their template projections too
-    rez.cProjPC(ix, :,:) = []; % and their PC projections
-end
+% remove spikes from the 0th cluster
+rez = remove_spikes(rez,rez.st3(:,2)==0,'below_cutoff');
diff --git a/preProcess/clusterSingleBatches.m b/preProcess/clusterSingleBatches.m
index 77ae4ddc..a0855594 100644
--- a/preProcess/clusterSingleBatches.m
+++ b/preProcess/clusterSingleBatches.m
@@ -178,24 +178,33 @@
 % sort by manifold embedding algorithm
 % iorig is the sorting of the batches
 % ccbsort is the resorted matrix (useful for diagnosing drift)
-[ccbsort, iorig] = sortBatches2(ccb0);
+[ccbsort, iorig, xs] = sortBatches2(rez.ccb);
+rez.iorig = gather(iorig);
+rez.ccbsort = gather(ccbsort);
 
 % some mandatory diagnostic plots to understand drift in this dataset
 figure;
-subplot(1,2,1)
-imagesc(ccb0, [-5 5]); drawnow
-xlabel('batches')
-ylabel('batches')
-title('batch to batch distance')
-
-subplot(1,2,2)
-imagesc(ccbsort, [-5 5]); drawnow
-xlabel('sorted batches')
-ylabel('sorted batches')
-title('AFTER sorting')
-
-rez.iorig = gather(iorig);
-rez.ccbsort = gather(ccbsort);
+% distance matrices
+subplot(2,2,1)
+imagesc(rez.ccb, [-5 5]); axis tight
+xlabel('Batches')
+ylabel('Batches')
+title('Distance Matrix, before sorting')
+subplot(2,2,2)
+imagesc(rez.ccbsort, [-5 5]); axis tight
+xlabel('Sorted Batches')
+ylabel('Sorted Batches')
+title('Distance Matrix, after sorting')
+% drift plots (in a 1D embedding)
+subplot(2,2,3);
+plot(xs);set(gca,'ytick',[]);xlabel('Batches');
+title('Drift Plot, before sorting');axis tight
+ylabel({'Manifold Position'});
+subplot(2,2,4);
+plot(xs(iorig));set(gca,'ytick',[]);xlabel('Sorted batches');
+title('Drift Plot, after sorting');axis tight
+ylabel({'Manifold Position'});
+drawnow;
 
 fprintf('time %2.2f, Re-ordered %d batches. \n', toc, nBatches)
 %%
diff --git a/preProcess/preprocessDataSub.m b/preProcess/preprocessDataSub.m
index 1add3c38..1f8f7ca1 100644
--- a/preProcess/preprocessDataSub.m
+++ b/preProcess/preprocessDataSub.m
@@ -74,7 +74,13 @@
 fprintf('Time %3.0fs. Loading raw data and applying filters... \n', toc);
 
 fid         = fopen(ops.fbinary, 'r'); % open for reading raw data
+if fid<3
+    error('Could not open %s for reading.',ops.fbinary);
+end
 fidW        = fopen(ops.fproc,   'w'); % open for writing processed data
+if fidW<3
+    error('Could not open %s for writing.',ops.fproc);    
+end
 
 for ibatch = 1:Nbatch
     % we'll create a binary file of batches of NT samples, which overlap consecutively on ops.ntbuff samples
@@ -103,7 +109,10 @@
     datr    = datr * Wrot; % whiten the data and scale by 200 for int16 range
 
     datcpu  = gather(int16(datr)); % convert to int16, and gather on the CPU side
-    fwrite(fidW, datcpu, 'int16'); % write this batch to binary file
+    count = fwrite(fidW, datcpu, 'int16'); % write this batch to binary file
+    if count~=numel(datcpu)
+        error('Error writing batch %g to %s. Check available disk space.',ibatch,ops.fproc);
+    end
 end
 
 rez.Wrot    = gather(Wrot); % gather the whitening matrix as a CPU variable
diff --git a/preProcess/sortBatches2.m b/preProcess/sortBatches2.m
index 15d4a36a..9aef3c80 100644
--- a/preProcess/sortBatches2.m
+++ b/preProcess/sortBatches2.m
@@ -1,4 +1,4 @@
-function [ccb1, isort] = sortBatches2(ccb0)
+function [ccb1, isort, xs] = sortBatches2(ccb0)
 % takes as input a matrix of nBatches by nBatches containing
 % dissimilarities.
 % outputs a matrix of sorted batches, and the sorting order, such that