what type of a video do you want? what i understand from your query is that for each time point you have a set of z-stack images. So, what do u exactly want in your video file?

I want to 3D render the z-stacks with maximum intensity projection, per time point first, and when I have all the 3D images of all the time points,  then I want to add them in a series for making the video in probable formats like AVI etc. 

Split the channels (Image, Color, Split Channels) so you have z stack time lapse of each channel individually.  Then use Z Project to make max projections of each channel stack.

Recombine the new projected time series with Image, Color, Combine Channels.  Now it will be in RGB and you can save as AVI.

Split and segregate the z-stacks for each time point. Then take each of the z-stacks and go to Iamge - Z porject - maximum intensity. You will get a maximum intensity projection for each of your time point from the z-stacks. in this way. Now go to Image - Stack - Images to Stack. You will get a stack with all the max. projections from each z-stack as a time series.Hope it works for u.

Thanks a lot. It worked.