I assume that you need the peak which are sharp and with high intensity. I made some changes in your code please have a look. Change threshold according to your need.
%Loading data
FileName = uigetfile('*.txt','Please select spectra:');
fid = fopen(FileName,'rt');
temp = textscan(fid, '%f %f %f %f %f', 'headerLines', 8, 'Delimiter',';','CollectOutput', true);
fclose(fid);
temp= cell2mat(temp);
wavelength = temp(:,1);
raw_counts = temp(:,2); % Background subtracted
dark_counts = temp(:,3); % Background subtracted
counts = temp(:,2)-temp(:,3);
threshold=2500;
% Finding peaks
[PeakValue, PeakIdx] = findpeaks(counts);
PeakIdx=PeakIdx(PeakValue>threshold);
figure(1)
plot(wavelength,counts,'b','LineWidth',2,'Markersize',6)
xlim([364 925])
xlabel('Wavelength (nm)')
ylabel('Intensity (arb. unit)')
x=wavelength(PeakIdx);
y=PeakValue(PeakValue>threshold);
text(x,y,num2str((1:numel(y))'))
the result for the above code is some what like this.
