Manual tracking / Chemotaxis tool problems

Hi all,

I’m having a problem with the manual tracking and chemotaxis tools in Image J. When i try to import the xls file from manual tracking into the chemotaxis tool it fails to read the file correctly and jumbles up the track numbers, rendering the files unusable. Initially this was a problem in Fiji and was solved by moving to image J but has now started in there too.

eg, In the chemotaxis tool, instead of reading the file as Track 1, Slice 1,2,3,4 etc… it reads as Track 1, slice 1, track 2, slice 1…track 1, slice 2, track 2, slice 2…

Does anybody know what is going on here/how to fix this?



It seems another user had a similar issue - see this older forum post:

I believe @Elias will be the best person to help you in this.

eta :slight_smile:


The Chemotaxis and Migration Tool is pretty picky when it comes to the data table import. Please send me your data table and I will see what I can do.


1 Like

Another year, another question about this!
I am having a similiar issue where the Manual Tracking data seems to be getting switched around upon import. It’s reading the slice number as the track number and the X position as the slice number. This is with data directly from the Manual Tracking output. When I try to make a tab delimited file in the format given by the manual, that also doesn’t work. I had a friend who regularly uses the plugin send me her “template” for the data, and pasting into there and saving as a tab delimited file with txt, xls, or csv extension didn’t work.

I also tried downgrading ImageJ to 1.48 without luck.

Were you able to resolve this issue with this user @Elias?

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.


1 Like

I checked the example from the Chemotaxis and Migration Tool from ibidi, I realized the result output from the Manual Tracking plugin in Fiji/ImageJ (ImageJ 2.1.0/1.53e; Java 1.8.0_172) is missing the first column. Fortunately, the first column is just a sequential row number, it is easily added with Excel.

With the added 1st column of row number, save the result table as tab separated value file. Now this tsv file can be used with the Chemotaxis and Migration Tool.

1 Like