Issues with Fiji error during tile discover

Usage & Issues
#1

Hello everyone,

I’m new to this online space, however I intend on immersing myself further in this community as my research has required the basic uses of ImageJ for a few years. However I have been increasing the complexity of my ImageJ usage and I have encountered some issues. If someone can assist me, it would be appreciated.

As a preface, I am using a Mac, and running the most recent software (Catalina 10.15.x). My microscope photos are being taken on an AmScope MU500, using the AmLite software. I have been saving my photos as .tif and .tiff. Additionally, I have very little experience with coding.

I’ve been attempting to stitch together my photos to give a large and high-resolution images for analysis.

I have strictly followed the steps outlined on the Stowers Institute for Medical Research on YouTube (https://www.youtube.com/watch?v=S54udQGGcS4). Yet I haven’t been able to stitch together my images and have received this error:

Stitching internal version: 1.2
**Loading (0, 0): /Users/myname/Desktop/Tif test/tile_1.tiff … **
ERROR: Cannot find file: ‘/Users/myname/Desktop/Tif test/tile_1.tiff’ - abort stitching.
ERROR: Error during tile discovery, or invalid grid type. Aborting.

I have tried “BigStitcher” and “MIST” with different issues.

Any assistance would be greatly appreciated as I’ve put in a significant amount of time trying to fix this, but with no success.

Thank you

#2

This indicates that your initial file path is wrong, so I would start there. If you are following the instructions for a PC too closely, it is possible that your file path is incorrect, as I believe Macs and PCs have to structure their file paths differently. You may want to look for some examples of Mac file paths in FIJI on the forum, there should be quite a few.

#3

Thank you for your reply, MicroscopeRA.

I’m sorry, I haven’t been able to find any resources after an hour of searching. Do you have a specific example that I can template? I may need slightly more guidance, as I am trying to learn but encountering road-blocks.

#4

Sorry, I don’t know offhand and have not used a Mac.

I have run into that error before, and it was when I was getting my file path wrong while thinking it was right. It could be a simple as your tif file ending with .tif instead of .tiff, it would be hard to say without knowing about the entire project/directory/file structure.

If you want to test things, try directly opening the file path using a macro.

#5

No worries,
Thank you for your suggestions, and I’ll get back to you if they work.

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#6

Hi,

as @Research_Associate already mentioned, it says that your file does not exist:

Double-check the path to find the issue. If it’s not obvious, start the recorder (Plugins>Macro>Record) and open that File manually (File>Open). What string is being recorded?

Also spaces in the path can be an issue. If so, surround the path with square brackets.
I by the way don’t think it’s a Mac versus PC issue here.

But in general: It’s really best if you just record your full stitching procedure. Then the paths are automatically correct.

#7

Hello all,
thank you for all the helpful replies. The error ended up being 2 issues: 1) syntax error; 2) jpeg file needed to be converted to TIFF

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