Hello. I’ve completed a trace for neuron, but now that I am finished, I need to save and I can’t. I go to the top left “File” tab on Fiji and there isn’t an option to “save” or “save as”; only export and import. My next idea was to try saving using the Mac “File” tab at the top left of the screen, which does support a “save” and “save as” option, but the file type options are not the types that I need. When I try to save as a .tif, it switches to .tiff and I can’t reopen my file on SNT and I’ve lost my work. Is there a certain way to save a traced MAX file on the Mac?
Welcome to the forum, @serenade
To save a tracing, go to File > Export As in the main SNT dialog as shown below:
These two options will export all Paths currently housed in the Path Manager.
There are two file formats in which you may save a reconstruction, .TRACES and .SWC
SWC is a widely used standardized format for representing neuronal tracings, and is supported by virtually all software that handles neuronal tracings.
TRACES is an SNT-specific file format that stores additional metadata such as channel, frame, and Path Manager tags associated with each Path, which is useful if you are tracing on multi-dimensional (i.e., 4D and 5D) images.
It is important to note that only the traced Paths themselves are exported, not the underlying image on which they were traced (the 3ds Max file in your case).
After you export either the .TRACES or .SWC file, you can load it back into SNT using the File > Import menu (e.g., File > Import > (e)SWC… or File > Import > TRACES…)
You may also simply drag the file onto the SNT dialog or the Path Manager and the import will occur automatically.
For more information regarding these formats, have a look at the “In which format should I save my tracings: TRACES or SWC?” question in the SNT FAQ
If you are unsure about which format to use, you could simply export a reconstruction in both formats (they have a very small storage footprint).