Merging virtual hyperstacks


While trying to merge two hyperstacks that are too large to fit in the RAM at the same time, I try to use virtual stacks. The problem is that after they are merged, both z and time stops functioning. I still says that the dataset contains correct z and time dimensions, but I can’t scroll throuh either. Also, if I save the merged hyperstack and open it in visualisation software like Imaris, it does not display correctly.

Is this a known issue, that virtual hyperstacks cannot be merged using Imagej?

EDIT: Could someone try to recreate this bug on their system to verify it? You need two 4D stacks that are too large to fit in the RAM at the same time. Open both of them as virtual stacks and try to merge them to a 2 channel 4D stack. Do you still have time and z, scrollable? For me, it only displays slice 1 on timepoint 1. Exporting them produces non-readable datasets.

I just tried to replicate this problem. Here is the start of a macro:

many = "many-planes&lengths=512,512,5000,10&axes=X,Y,Z,Time.fake";
lots = "lots-more&lengths=512,512,5000,10&axes=X,Y,Z,Time.fake";
run("Image... ", "source=" + many + " crop=false groupfiles=false mode=Cell");
run("Image... ", "source=" + lots + " crop=false groupfiles=false mode=Cell");

But what command are you using to merge the hyperstacks? “Merge Channels…”? Indeed, I cannot get that command to merge such virtual stacks at all.

Exactly. I use “Merge Channels” for merging two hyperstacks that I have opened with the Bio-Formats “Import” function. The virtual hyperstacks are actually put together as one image, but when I try to scroll through time or z, nothing happens. It works fine as long as it’s not virtual stacks. Problematic with huge datasets that won’t fit in RAM.

Is there another way of merging them that I’ve missed? I can’t really comment on your macro since I don’t know that much about how to write them.

For what it’s worth, I filed imagej/imagej#134 to track this problem. Sorry I don’t have a solution for you.

Thanks alot! No, problem, you have been very helpful. Getting a new workstation with 128 GB RAM which should alleviate the problem a little bit. Would be great if the functionality was there though. Hopefully someone will fix this bug(?), fingers crossed.