Error message when processing Neuroanatomy

I’m the local IT support, I don’t use Image J, or know anything about. I’ve re-installed Fiji Image J and successfully installed the Neuroanatomy plug in as the user requested She ran the plugin on an image file and received the attached error message. Any ideas as to what the issue may be?

The screenshots don’t appear to be showing.
User is running Win 10 x64, ImageJ 1.53c

the user is stating it’s supposed to look like attached below. It does not show like that on her PC.

Welcome to the forum, @blancop!

Judging from your description, it sounds like the user is attempting to use SNT (formerly Simple Neurite Tracer), which is part of the Neuroanatomy toolbox. Is the user able to open this ND2 file in ImageJ prior to starting the SNT plugin, or does the issue only occur when attempting to load this image into SNT? I am not familiar with the ND2 format, but from a quick search it seems as though extra steps are needed to open this format in ImageJ. See How to open an ND2 file properly?

@tferr any thoughts on this?

@blancop, pretty much @arshadic’s recommendation. Proprietary formats are not handled by ImageJ directly but rather by other plugins, remarkably Bio-Formats. The solution is to 1) export the data in the Nikon software as (OME) tiff, or 2) Load the nd2 file using ‘Plugins>Bio-Formats>Bio-Formats Importer…’ before starting SNT. Abolish the usage of proprietary file formats altogether would be my upstream advice.


thanks, this didn’t solve the user’s issue. The error still persists when she runs the plugin. Any other ideas?

Hi @blancop

Is this after successfully loading the ND2 file into ImageJ using the Bio-Formats Importer?
It would be helpful to know the precise sequence of steps the user tried, along with any error messages, stack traces, or screenshots demonstrating where the error is occurring.
Have they tried converting the ND2 file to a TIFF before loading the file into ImageJ?

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@blancop : Coincidentally, this should no longer be an issue. See ImageJ SNT plugin - can't open my image file