Migration and Chemotaxis Tool Troubleshooting Problems

I’m currently looking at cell migration and directionality of cells after spontaneous cell fusion. I’m trying to do very similar analysis to that done in Dr. Felicite Noubissi and Dr. Ogle’s Paper titled “Apoptosis-induced cancer cell fusion: a mechanism of breast cancer metastasis”. I’ve been in contact with Felicite to understand her work flow and protocol and we are now both having problem using the Chemotaxis tool. Once we move to the Migration and Chemotaxis tool (now only known as the Chemotaxis tool within FIJI) we can’t get the data to actually load within the tool. I have looked at the documentation and it mentions that as long as you track or Manual track using FIJI you should have no problem which is my current workflow, but it’s not working. Do you know a way to fix this problem or a new way for formatting (and the file type) the data to continue with the analysis? Any help would be appreciated.

Dear @Chitw015,

Did you take a look at Chapter 4.1 Import Data of the documentation? Does the data that you are trying to import adhere to the conventions described in that chapter?

In addition, I have invited the authors of the plugin to this thread. They might be able to provide further insights.

Best,
Stefan

Dear @Chitw015,
could you please upload an example file that you are trying to upload in the Chemotaxis Tool?
I usually save the manual tracking in .txt and I can import it in the chemotaxis tool.
Something like that:
test_manual_tracking.txt.zip (1.4 KB)
It comes out like that directly from the manual tracking tool but you have to save the results table as .txt

Hoping to be helpful
have a nice day,
Emanuele Martini

Hi Casey,

please send me one of your example data files to my email addres (ehorn@ibidi.de). I will check. The Chemotaxis Tool is quite picky with the data table import. It the import file does not fit 100% it won’t work.

Thanks for the invitation, Stefan!
Elias

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It’s not letting me upload the files. Something about how new users can’t upload. If you send me an email I can get them to you. My email is chitw015@umn.edu. The Mac I’m using automatically saves the manual tracking files as .csv files which look like excel sheets. I can manually change it to .txt and then I can get the data uploaded into the tool but can’t get it to plot. That may be me missing some little detail though I’m going back through the documentation today.

cannot you get only the plot or also the stats like mean velocity and so on?
have you applied settings?

have a nice day
Emanuele

After referring to the documentation, I think I got it working. It is now giving me a directionality value and track plots. I just need to check with my collaborator to see exactly what her setting were. Thank you so much for your help!!

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Great! How exactly did you do that? It would be really helpful to post your solution so that someone who stumbles over the same issue can solve it as well.

Best,
Stefan

How were you able to get this to work ? I have run into the sample problem where my files are being saved as .csv and the chemotaxis tool will not recognize them.

Hello, I also meet the same problem. I download the thest_mannual_tracking.txt and import it into the chemotaxis tool, but it still shows error like “formate is not supported” as shown in the following picture. can you tell me the reason?


Looking forward to your reply
Best regrads,
Wenxiu