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Zebrafish Lab

Apr 28, 2023, 10:17:33 AM4/28/23
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Hi! I'm trying to run 
idtrackerai_csv path/to/session_[SESSION_NAME
without success, in python. Which modules are needed to be imported for this function to work and could I have an actual example of how you would run the code? Python newbie here, so I've probably missed out something simple. Thanks for the software!  


May 2, 2023, 6:56:21 AM5/2/23
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All commands like
  • idtrackerai --load ...
  • idtrackerai_validate /session_...
  • idtrackerai_csv /session_...
  • idtrackerai_video /session_...
are terminal commands. This means that you have to run them on the Anaconda prompt (or in the terminal if you are using Linux or custom idtrackerai installations).

In Windows, you have to:
  1. Open Anaconda Prompt (search in your installed programs).
  2. Type "conda activate idtrackerai" to activate the Conda environment where your idtrackerai installation is.
  3. Type any of the commands on the list above to run an idtrackerai program.
You don't have to write any Python code to run idtrackerai nor any of its additional tools.

Hope that helps, keep asking if you need more help.


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Zebrafish Lab

May 3, 2023, 4:11:38 AM5/3/23
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Thank you, that was useful. I think my main problem though was that I was running an older version of idtrackerai, I updated it to version 5 and it is running now.

A related question, to get data like average speed per individual in csv format (for combining with other data and analysing in different stats softwares), which method would be appropriate to use? Can the package Trajectorytools also, in addition to making lovely plots, output this summary data? Or should one calculate these things manually from the coordinates in the trajectories.csv file?      


May 4, 2023, 5:48:23 AM5/4/23
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Happy to hear that it's working for you!

As I'm not developing nor using trajectorytools, I cannot give you much information about it and which specific tools it has. But anyway, while trajectorytools can help you with simple and fast analysis, my personal recommendation is that you write your own scripts (in Python, R, Rust... even Microsoft Excel!). The trajectory files are easy to load in Python and, once converted to csv, also in any language.

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