While you may want to think about a cleaner way of dealing with the plot (e.g., plotting in the same figure window and saving), this'll do what you need:
% find the index of all the 1's in the first column
idx = find(data_counter(:,1)==1);
% loop over the sets
for ind_set=1:length(idx)
% figure out where the current set starts and ends
% you already know where it starts
start_ind = idx(ind_set);
% if this is the last set, it ends at the last row
if ind_set==length(idx)
end_ind = size(data_counter,1);
% otherwise, it ends one row before the next set starts
else
end_ind = idx(ind_set+1)-1;
end
% loop over the columns
for ind_col = 2:size(data_counter,2)
% option A: open a new figure so nothing gets overwritten
figure
% plot the correct slice of data
plot(data_counter(start_ind:end_ind,ind_col))
% option B: save each plot as it is created
print("Fig__set-"+ind_set+"_col-"+ind_col,'-dpng')
end
end
