Import .h5 file as virtual stack

fiji
hdf5

#1

Is there any way to import a .h5 file as virtual stack? I am having issues to import big files (I got an error of large dataset) even if a have 256gb of ram almost all available…


#2

Hi @pgarciac

How big are we talking?

We use n5 for this in our lab. It even has an h5 wrapper.
Unfortunately, at first glance the ImageJ plugin part of n5 doesn’t play nice with h5.

I’ll have a look at this later.
John


#3

It depends on the dataset, but broadly are image stacks of 32 bit, size about 3000x3000x4000 the biggest one.

I am very newbie with Fiji (I usually program everything in Matlab) so no idea about n5. I’ll take a look. Thanks!