you can analyse peak time, baseline, peak, from peak to %(50-75-90) relaxation, area, tau, departure velocity, return velocity etc.

if you can converts your files into ZPT form ionoptix gives you results much more you need.

Thanks a lot for your suggestions. Looking for it.

Hi Apurva

What is the nature of the calcium release events? Are they calcium sparks or "full" global calcium transients? 

The data shows that there are calcium transients which peak at periodic intervals and their amplitude decays over time. There are sustained increases in calcium levels as well which once rose remained sustained for as long as 20 min or above.

@Yusuf: I checked but I guess ionoptix is not a free software. We do not have it in out institute. Can you please suggest me a substitute for this purpose.

unfortunately,I have no other analyse  program to suggest. At least try to find demo version of ıonoptix then I would help you in detail.

best wishes

You might want to check this paper and the code they provide.

http://www.ncbi.nlm.nih.gov/m/pubmed/19778505/

Hi Apurva,

If they are global calcium transients I usually measure and analyse baseline, peak, decay tau, rising velocity and duration from peak to baseline at several %. Most of the adquisition softwares allow you to export data as ascii or txt.

In my case, to analyse calcium data I use clampfit, a software used for electrophysiology and available for free at molecular devices website (http://mdc.custhelp.com/app/answers/detail/a_id/18779).

Just import the txt data and use the event detection menu to get all measurements in which you are interested.

Thnk u . thnk u ... seems I got really really helpful suggestions.... 

@Jose and @Asaph: Would you also like to guide me on this another question related to calcium imaging experiment...

https://www.researchgate.net/post/Can_you_help_me_designing_a_calcium_imaging_experiment

Dear Apruva,

This is a very important topic at the frontier of our knowledge about the brain.  I suggest to analyze the amplitude modulated waveform the same way that audio engineers analyze sound. For a general view of the functions of calcium waves please take a look at the corresponding sections of the attached paper.

Thanks a lot @Alfredo.. looking at the papers...

Fiji/ Image J can be effectively used to analyse calcium signals

Check this thread - easy enough

http://akiramuto.net/archives/148

Hi Apurva,

You can check my recent paper for the Ca imaging data analysis.

Article Comparison of Calcium Dynamics and Specific Features for G P...

Although, this paper is based on big data analysis and pattern finding within the data but you might get the IDEA for your data analysis. Generally, I do the unbiased analysis using MATLAB. You can also try. Let me know if you have any specific question. I will be very happy to help you.

Good Luck.

Thank you. Looking into it..

I am new into calcium imaging experiments. i need to analyze the data from the experiments for the peak respond to capsaicin, slope respond, are of slope etc

but i odnt know how using the right and easy software to do it

Dear Wance Firdaus,

Decay time can be calculated if the response has one peak. Also, you can calculate the time of peak and amplitude of the peak and draw the statistics. I will not recommend you to calculate the Area of slope/area under curve as this analysis will highly mislead you to completely different connotation, and simple justification for that is, if you see the figure I attached, clearly, there are three different types of response we can see but by calculating the AUC, you might end up having the same value for all.

For more articulate and advance analysis, you may follow my two articles:

Article Comparison of Calcium Dynamics and Specific Features for G P...

Article Confocal Imaging and k-Means Clustering of GABAB and mGluR M...

Should you have questions, do not hesitate to write.

Best,

Rishi

Hi Rishi

Thanks for you valuable response but i am very new in this area and i need to get all the number of the peak. I did experiments using hamamatsu camera and easy rate pro. then i got the number and paste them into excell. how could i analyze everysingle data , is there any free software to download line NeuroCa or clamfit. Thanks

Wance

Hi Wance Firdaus ,

I use MATLAB. You may use R instead but you need to write your own script.

Best,

Rishi

Hi,

I'm new to calcium imaging and recordings. I recently got some calcium imaging data from Mosaic software which they are delta F over F and some event traces. I need to find the distance correlation between the raw images of the cells and also delta F over F correlations with MAYLAB but I have no idea how to do it. Please someone help me through this.

Best,

Oveis

Hi Oveis Hosseinzadeh Sahafi ,

You can go through my answers in this trail. Still if you have any question, you can write again.

Good Luck.

Best,

Rishi

Rishikesh Kumar Gupta Hi Rishikesh !!

I found your answer very helpful in analyzing my live-cell calcium imaging data.

Briefly, I stimulated my cultured neurons with NMDA (The stimulus), I observed an instantaneous rise in Calcium signal (the fluorescence peaks). and then there is a slow decay. For the decay part, I am quantifying the Time constant of Decay, Tau. I am not sure whether I should look at the rising part too. No one looked at the rise time in the literature also. Is it because the rise was instantaneous?

I am attaching a figure file (for the kind of calcium signal i am getting in my imaging experiments after stimulation)

Hope you can provide an explanation for why people haven't looked at the rise time in such a case..

Hi Tushar Arora

Thank you for your question.

First of all, there are two different terms: Time constant- the time elapsed after 63% of max has been reached, which is generally represented as τ (tau). The reciprocal of the time constant is called the decay constant, which is usually described as λ (lambda), which can also be enumerated as the time elapsed after it has fallen to 37% of max.

Now, If you look into details, the resistance across the membrane is a function of the number of open ion channels, and the time constant is used to describe the rise or fall of the response magnitude in the order of application of agonist or antagonist. Moreover, as you said, the opening or closing of ion channels is very instantaneous, and most of the cases, it reaches the max value in very few milli-sec. Nevertheless, this is not always the fact; for example, in electrophysiology, researchers measure the miniaturized current (as shown in the figure), and in this case, they prefer to calculate rise time (time constant).

Let me know if you have any other specific questions.

Best,

Rishi

Hi everyone,

I am new to ImageJ and have a project to write a macro in which all my calcium sparks analysis be done in ImageJ. So far I just automated the BG subtraction and normalization, ploting my data correctly.

I am just now stuck at this point. because I need to make curve fitting in order to drive the calcium sparks parameters such as rise and decay time, FWHM, FDHM and so on.

Any help, source or guide is highly appreciated.

Best

Mahsa

Hi Mahsa Shakouri

If you can export your data in excel after normalization, you can use any curve fitting tool. For example, in this given link: https://www.mdpi.com/1422-0067/21/3/842/pdf , if you look into figure number 1D, pretty much similar kind of analysis has been done as you would like to do for your data.

I also perform this such analysis using MATLAB, and I find it pretty easy.

Good luck!

Best,

Rishi

Some of these features are measured by https://github.com/vladscript/FinderSpiker and others such as coactive groups of cells and beyond if your input data are raw fluorescence traces in columns for each cell in the fifth row.