Try flattening the signal by subtracting that red trend line. Then set the values of the signal below the threshold to zero and then call findpeaks()
smoothedSignal = movmean(signal, 101);
flattenedSignal = signal - smoothedSignal;
flattenedSignal(flattenedSignal < someThreshold) = 0;
[peakValues, indexesOfPeaks] = findpeaks(flattenedSignal);
Attach your data in a .mat file if you need more help.