Dear Michael,

                       I use imagej with the LOCI bioformats importer to open LSM files without any problems.

http://downloads.openmicroscopy.org/bio-formats/5.3.3/

This should work fine in Fiji as it already has the bioformats plugin as I understand however you may want to try with imagej itself just incase there is an issue with Fiji. The other thing you could try is to increase the memory allocation that imagej is allowed to use. I am not sure if it is the same in Fiji but in imagej go to : Edit-Options-Memory & Threads. Here you can adjust the amount of RAM that imagej can use. It would usually give you an error message if memory was the issue but as you mentioned the files were large this is worth a go. The last resort if you are still unable to open the lsm files would be to write a simple macro in imagej to stitch the single images generated in Zen into stacks.

I hope this is useful and good luck!

Graeme  

Dear Micheal,

We also use the Bioformats plugin at our Labs (with ImageJ and FIJI) and i am not aware of ever having this problem!

Yes the ressource allocation steps should be the same for ImageJ and Fiji.

You could also try to export your Files with ZEN (if i remember correctly this should give you single TIF files) and restack them with ImageJ/FIJI

I hope this helps

Simon

Have you tried saving as .czi in ZEN and opening that in Fiji? Also, 14GB is quite huge, make sure you have enough RAM usable by Java. Or try to downsample on loading or open as a virtual stack... (not sure BioFormats support that).

Thank you for all your suggestions.

Unfortunately, I had already tried Bioformats plugin. Interestingly, I had the same problem using Imaris software: The picture shifted with that line coming in, as you can see in the screen shot.

I had also tried saving them as .czi files (same problem as with .lsm files), and tried restacking the single .tiff files that ZEN can export (this was too time consuming).

Here's the solution I came up with: ZEN BLUE Desk (not Lite!) is capable of exporting lsm files as one single ome.tiff (check "big tiff" in export options). This file can be read by ImageJ and Imaris without problems.

I had this problem more than once, and using various microscopes and working stations (separate institutes). I can't make sense of it, but am happy to have a work-around. Anyways, I appreciate the help.

We can not open our Zeiss .czi files in Imaris. I tried your suggestion to export them as OME.TIFF file but the OME.TIFF file generated is not recognized in Imaris (version 7.5.2). Do you have a suggestion? Many thanks in advance.

Monique

Do you use Zen Blue or Black?

Weird that Imaris doesn't even open .czi or ome.tiff. Maybe try saving the image as an .lsm file in Zen, and then opening it with Imaris?