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Parametrize Calcium Signals

version 1.0 (734 KB) by Laurent MacKay
Characterize transient calcium signals

2 Downloads

Updated 12 Oct 2016

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Automated characteriztion of single and multi-peaked transient calcium responses from time series data. Signals are decomposed into drift and response components and the entirety of the signal is reconstructed using a mathematical model of a transient response and drift. Measures time of onset, activation time (10% to 90% of total amplitude),amplitude of response, full width at half maximum, decay time constant. For oscillatory multipeaked responses the algorithm attempts to separate coherent oscillations from completely stochastic ones and for the full set oscillations as well as the coherent subset reports the number of oscillations, period of oscillation (averaged), standard deviation of the period, magnitude (averaged), full width half maximum (averaged), duty cycle (averaged), and the length of oscillatory persistence.
Signals can be stored in an excel sheet, and the whole document can be processed with the command:
characterizeDocument('example.xlsx');

Cite As

Laurent MacKay (2019). Parametrize Calcium Signals (https://www.mathworks.com/matlabcentral/fileexchange/59693-parametrize-calcium-signals), MATLAB Central File Exchange. Retrieved .

Comments and Ratings (5)

HI Laurent,

I padded the example signal with the initial and final signals, trying at most 8 seconds each end. Same error of not enough drift. If it helps, I'm using Windows 10 64-bit OS with Matlab 2016a.

Best,
Brandon

Hi Brandon,

I am currently working to overhaul the software. Thank you for mentioning this error, I will see if I can reproduce it, but what I can suggest is to pad your signal with some constant values at the beginning and end then rerun the code and see if the same thing happens.

Laurent.

This sounds like a great program, however, I am unable to get the example data to run properly. During parameter characterization, I am receiving the display "not enough drift." While I know that this is being prompted from line 371 of the parameterCharacterization.m file, I am unsure of how to resolve it.

I really like the idea behind this program as I don't think there are other automated analysis programs that can provide as much information as this one can. I've gotten it to work for their example that they provide, but incorporating my own files has proven more difficult. I give it 3 stars for the potential and ability but knock it for the lack of clear documentation. If the documentation improves, I'll update my score.

Updates

1.0

Description Edits

MATLAB Release Compatibility
Created with R2016a
Compatible with any release
Platform Compatibility
Windows macOS Linux