LINCellularNeuroscience/VAME

Making VAME compatible with SLEAP?

juliagorman opened this issue · 6 comments

juliagorman commented

Hello,

Is there a way to make VAME compatible with the SLEAP file outputs instead of DLC? My lab uses SLEAP instead.

Thanks!

Lauraschwarz commented

i saw that issue #100 might help with being able to load SLEAP output .h5 files into the egocentric_alignment function.
i always assumed VAME was compatible with SLEAP?

juliagorman commented

Hm okay I havent tried running with SLEAP yet, but I assumed it wouldnt work because the data strcuture of SLEAP h5 files are different than the h5 files from DLC

Lauraschwarz commented

i have tried it today, and i have struggled. especially the second step to align the DLC output egocentrically specifically asks for a .csv file...

in the VAME paper it is mentioned that it should work with SLEAP as far as i remember. i did some research and found this: talmolab/sleap#1089 to convert your Sleap .h5 into a .csv (as far as i understood)

i am still very new to all this. so please take my "help" with a pinch of salt.

Lauraschwarz commented

Heya Vame- Team, i was wondering whether there is an update on this issue? are there any resources that @juliagorman and me are missing? thank you very much in advance for any reply :)

Lauraschwarz commented

Hi @juliagorman have you had any luck with this? just thought i'd check in with you since you seem to be in a similar situation to me :)

akesner1 commented

I also want to do this. I am trying to write a basic python script to just reformat SLEAP .csv to look like DLC .csv. Anyone have any other ideas? Does the VAME team have any idea if this is something that could be added?