A scatterplot matrix is for if you have several equally-sized columns that you want to plot against one another. That doesn't sound like your problem. It sounds like you have 64 sets of data that you want to plot separately.
Does this do it:
% number of cells
N = 4;
% generate test data
for ind=1:N
X{ind} = rand(randi(10),randi(10));
Y{ind} = rand(size(X{ind}));
end
% create a (here) 2x2 subplot arrangement
tiledlayout(sqrt(N),sqrt(N))
for ind=1:N
% in a particular subplot
nexttile
% scatter plot all Y points vs X points
scatter(X{ind}(:),Y{ind}(:))
end
(if you have 64 sets of data, where you want to create a scatterplot matrix for each set... may I recommend a separate figure for each plot so you can actually see anything?)
