Hey,
If I understood correctly your question, you should use a cell array due to numeric array limitations which is that numeric array has to have equal number of columns in the same row and vice versa. Iit is not possible to do it with a numeric array because there might be different number of peaks in each row. You can squeeze your peaks and locations into a single element of cell array for each row like shown below.
pks = cell(size(dff, 1), 1);
locs = cell(size(dff, 1), 1);
for i=1:size(dff, 1)
[pks{i},locs{i}]=findpeaks(dff(i,:), 2, 'MinPeakHeight', threshold(i));
end
