Avizo subsampling while reading

Dear All,

I would like to read multiple tif images that form a 3D object in Avizo. I hit the out-of-core threshold limit and Avizo suggests lda, read as external data or read complete volume into memory.
I cannot use lda because I need all the details of the images.
To keep all the details and be able to read as the 3D object, I have to subsample while reading the data. Could anyone please suggest me how to do that or refer me to some forum for Avizo- I searched on google both in English and French; couldn’t find such forum.
Bests, Hattie

What is the total file size of your data set? Have you tried the “read complete volume into memory” option anyways?

Hi @Atha
Apologies for replying very late - I just joined image.sc.

We once had a forum, but found it difficult to moderate, I hear. This predates my time with the group. We now encourage users to directly contact us at FRBOR.3d_hotline@thermofisher.com

Avizo can handle image data larger than your available RAM, but generally it is better to have enough RAM to at least hold your data in memory for image visualization. There are many strategies for dealing with this issue:

  1. If you have a stack of similar images, you could create a recipe with Image Stack Processing and run that recipe on files from disk one at a time using the Process Stack on Disk module.
  2. You could save the data as an LDA formatted file (what the program is asking about when you try to load) and load this file. This requires an extension to the software, XLVolume (for now).
  3. Since it is a stack, you may try viewing only some of the slices - few enough that the subvolume will fit into memory. Not ideal, but could meet your needs in the short term.
  4. Consult this video for more info on loading image data in Amira and Avizo: https://www.youtube.com/watch?v=wxIYOYACdpA&feature=youtu.be