Use matlab function max() are not enough?

One quick fix would be to do -diff(sign(diff())) on the vector with your data. It will give you both the peaks and dips, but to get just the peaks, let's say that you called the resulting vector from the above operations cpeaks, then you can do cpeaks(cpeaks

have you tried ImageJ? We've had good success with it:

https://www.researchgate.net/post/Can_anyone_recommend_a_software_imageJ-plugin_for_analysis_of_in-vitro-Ca-Imaging_in_neurons

Matlab has a function called findpeaks, that allows to mark peaks and set some criteria for finding them. Just check the matlab documentation.

Hope that helps.

As Stefan said [pks,locs,w,p] = findpeaks(data) will find the peaks, their location and space and amplitude.... I have used it for very similar usage.

Dear Olga,

I am not very familiar with the term (Ca2+ signal) that you have mentioned in your query. But the fig. appended therewith provides some idea relating your question. If u want to quantify 'the amplitude and the duration of individual waves', Wavelet analysis may be a good solution. Otherwise for simply finding out the dominant peaks (Both positive and negative) you can apply the peak analysis for your data. Several computer programs are available for these tasks. But my choice is Origin Pro for both of these applications (wavelet analysis and peak analysis). Links are given for your information.

for wavelet: http://www.originlab.com/doc/Origin-Help/Wavelet-Transforms 

for peak analysis: http://www.originlab.com/doc/Origin-Help/PeakAnalyzer-QS#Peak_Finding 

https://www.youtube.com/watch?v=Y8nVlO8z02o

Hope this will help!

Dipanjan