Compressing z-stacks

Hi all,

Does anyone know if there is a way of compressing a z-stack, but keeping it intact as a stack please? I have a lot of very large images (some as big as ~40 Gb) which consist of a couple of hundred confocal tiles stitched together, and 10-20 z planes per tile. Such large files are unwieldy, and I cannot cut them up because I’m tracing neurons (in a different programme - Neurolucida) that span the entire image.

I can save each individual z plane as a JPEG or PNG using Save as → Image Sequence, and then use Images to Stack to reconstruct a stack, but it seems inefficient. Is there a better way?


Hi @rhamnett,

You might want to try saving into the OME.TIFF format, which supports both pyramidal images and various compression options.

If you’re using ImageJ, you will need to install the BioFormats library or else, just use Fiji which has it pre-bundled.

At that point, you can use [ File > Save As... > OME.TIFF ] and during the save options select the type of compression you would like to use (generally I would suggest a non-Lossy option):

Hope that helps.

Hi @dnmason

Thanks for your reply. While that does sound like it would work, saving as an OME.TIFF is taking an incredibly long time for my test image (I’m 15 mins in and it’s only half way there. Saving as a regular tiff would take a second or so). It seems to be the same problem that has been reported before here: Bio-Formats ome-tiff write time issue / bug? - #15 by sebi06 but it doesn’t look like there’s a solution for FIJI at the moment.

Do you also have this problem when saving z-stacks as ome.tiffs?