Alright, here is what worked for me.
I had old datasets from years ago that I checked and worked with both FIJI and ImageJ running the Chemotaxis tool – so the problem is not the version of Fiji/ImageJ. A dataset from the manual tracking plugin from 2013 was able to be imported and produced a normal, expected output for FMI/Velocity/Plotting paths.
I took my data from my 2019 dataset saved directly from the manual tracking plugin, and copied it into the framework of the 2013 file using excel. I saved it as a tab delimited text file. This worked. Saving the 2019 dataset from the manual tracking plugin as a tab delimited text file did NOT work in either Fiji or ImageJ v1.47.
This leads me to believe there is something different in how the manual tracking files are compiled. The only thing that stood out to me was that my old files had a different character appearing next to the header “track n” and “slice n” a slash (ｰ) as opposed to a degree “°”
I tried removing the “°” symbol as well as replacing it with the slash and resaving. This did not work. I will see if there might be another way to suss out hidden information that could be changing how the files are being read.
I will update if I get any further.
edit: 8/22/19 5:37 PM
I found that opening the non-working files in notepad and removing any characters in lines after your last result line produced working files! The ° signs could be left in and did not affect the ability of the plugin to read the file. After removing any extra characters after the last line of data, I saved the data as a .txt. Opened and read fine.
Example of what your results file should look like in notepad. The leftmost column (1,2,3,4,5,6…) is crucial.