Data structure

[roaldarbol]

Hi @VioletteChiara!

I'm writing an R package for analysis of animal movement from an array of different sources (pose estimation, centroid tracking, trackball/treadmill) and would love to support AnimalTA. I write reader functions for each data source, along with some validator functions that ensures that the files really are in the format that the user thinks they are. I received some single-animal data from a friend that uses AnimalTA (I haven't had time to try AnimalTA myself), and I'm wondering whether that is also valid for multi-animal data? Or are the data headers different when there are multiple individuals? So whether it is something like Frame, Time, ID, x, y or rather Frame, Time, x_1, y_1, x_2, y_2 when there are two individuals?

Additionally, can I expect other column values inside an AnimalTA data frame?

The package is currently called trackballr, but will change name to animovement one of the following days. I collaborate with the team making the movement Python package, so once I've gotten the reader and validators implemented it would also be a smaller task for them to support it. :-)

All the best, Mikkel 😊

[roaldarbol]

Oh, and I can see that the x/y columns in the dataset I received are called X_Arena0_Ind0/Y_Arena0_Ind0. Should I take that to mean that there can be multiple arenas and individuals, and that they would be added as extra columns? Maybe if you have some sample data of a small range of use-cases you can share that with me? :-)

[roaldarbol]

Does the user themselves specify the FPS then? It was more since there was no other temporal units than frames - how would it know how many frames there is in a second? (I'm quite sure both DLC and SLEAP only express frames, not seconds unfortunately). In which case, the only way to get the actual time is by reverse-engineering from the speed. Maybe it would be worth adding time as a column if FPS has been specified? Would make synchronisation with other data sources easier too. :-)

EDIT: I was reading your Detailed coordinates comment above, where it doesn't say Time - but I noticed it does in the previous comments, I think that's what confused me. Is Time always present in all exported data frames?

Ah, that makes sense! Good to know about that special case too! Is the reason that they're actually still being tracked in the entire frame, but you only keep observations inside the ROI? (That's just me being curious) :-)

[VioletteChiara]

The FPS is extracted from the file metadata (can also be modified in case of corrupted metadata), but the user can change it later (the program will then do a subsample of the frames).

Yes, it's my bad, I wrote wrong in my previous comment (sorry). The time is expressed in Frames for raw and corrected coordinates, but in Seconds for the Detailed data (where the speed is also mentioned).
To be honest, I thought that people would use the "Detailed data" for exportation rather than the raw or corrected data, but that does not seem to be the case. So it is a good idea. I can add one more "Time" column in the future.

Regarding the entrance data, there are two kinds of ROIs: the arena itself, which is where the track data are kept, and the entrance area which is from where we expect the targets to enter the arena. So they are indeed actually tracked outside of the arena (main ROI) but not everywhere else, only in the secondary ROIS (entrance area).

[roaldarbol]

Ah, that makes a lot of sense, thanks again for the thorough replies, amazingly helpful! BTW, I really like your development approach which seems focused on features the users ask for as opposed to what you think users want - it's a breath of fresh air - makes me happy to recommend AnimalTA to others!

[VioletteChiara]

Hi! Yes it is indeed the way the program is evolving, I try to encourage users to give me feedback and suggestions and if those are feasible I implement them in the program.

[VioletteChiara]

And thanks for the recommendations!