Timepoint z-stacks from Hyperstack

[Michael Doube-3]

Hi all,

I am looking for an existing solution to save a sequence of stacks from
a hyperstack.  It has been possible for a long time to save a sequence
of xy slices from an xyz stack, but I want to save a sequence of xyz
stacks from an xyzt hyperstack (and additionally in Raw Data format).

Does anything already exist, or am I stuck with my current hacky
solution: exporting all xy slices from the hyperstack and sequentially
importing image sequences and Save As raw?

Cheers,

Michael

[dscho]

Hi Mike,

On Thu, 18 Aug 2011, Michael Doube wrote:

> I am looking for an existing solution to save a sequence of stacks from
> a hyperstack.  It has been possible for a long time to save a sequence
> of xy slices from an xyz stack, but I want to save a sequence of xyz
> stacks from an xyzt hyperstack (and additionally in Raw Data format).
>
> Does anything already exist, or am I stuck with my current hacky
> solution: exporting all xy slices from the hyperstack and sequentially
> importing image sequences and Save As raw?

How about a simple macro which loops over all frames and uses Reduce
Dimensionality (with the "keep" checkbox checked), then saves the stack?

Ciao,
Dscho

[Michael Doube-3]

>> Does anything already exist, or am I stuck with my current hacky
>> solution: exporting all xy slices from the hyperstack and sequentially
>> importing image sequences and Save As raw?
>
> How about a simple macro which loops over all frames and uses Reduce
> Dimensionality (with the "keep" checkbox checked), then saves the stack?

That should do it, cheers!

Michael

[Michael Doube-3]

>> How about a simple macro which loops over all frames and uses Reduce
>> Dimensionality (with the "keep" checkbox checked), then saves the stack?

dir = getDirectory("Output location");
name = getTitle();
Stack.getDimensions(width, height, channels, slices, frames);
setBatchMode(true);
for (f = 1; f <= frames; f++){
    Stack.setFrame(f);
    run("Reduce Dimensionality...", "slices keep");
    saveAs("Raw Data", dir+name+"_t"+IJ.pad(f,3)+".raw");
    close();
}