Bio-formats not opening all z-stacks of nd2 file

I’m having trouble opening .nd2 files that have many z-stacks (~100) with 4 color channels. I’ve never had an issue like this with any of my other .nd2 files. When I try to open the file I get the bio-formats import options like normal, then after that it seems to think that the image has multiple series which it doesn’t. I thought I was getting around this by opening all the series and concatenating but for some files it gives me an image that has 30 z planes rather than 100.

I’ve tried reinstalling the newest version of Fiji.
I’ve tried changing all the bio-imports options.
I’ve tried disabling chunkmap in the plugins configuration.

Nothing has helped which is super frustrating. Any help would be greatly appreciated!!!

Hi @Jean_Smith_Ashby, we have seen some nd2 with swapped dimensions (most notably timepoints detected as series), does the number of series you are seeing match with any of the other dimensions?

If you have a sample file which you are able to send for testing you can upload it to

1 Like

The number of series seems to match the amount of z-stacks that fiji thinks the file has (even if this is not accurate) - what’s odd is that some files will open as 30 series and others as ~100, even though these images were taken with the exact same settings.

I’m uploading a sample file right now that should have 101 z stacks and opens as 30 series/z stacks.