animal_calibration usage

[francescovaccari]

Hi! I am using DLC + anipose in our lab, but unfortunately the 3D reconstructions are not satisfactory. I think it mainly depends on Anipose, as DLC 2D tracking seems quite accurate.

Ours is a 6-camera setup (Daheng Imaging) that records video synchronised by an Arduino generated external trigger (we checked the frame synchronisation and it is perfect). We perform a Charuco calibration (2-3 min at 100 FPS) before each session and sometimes the calibration matrix comes out normal, sometimes (actually, most of the times) it doesn't. Repeating anipose sometimes solves the problems, sometimes it doesn't, so I was thinking as a second line of counter-measure to try animal_calibration after the first Charuco calibration (since the 2D tracking seems to be of good quality, it should also be useful for calibration).

I modified the anipose pipeline to fit our directory system and data storage, thus I call aniposelib functions directly from my scripts, but I can't find which part of the aniposelib package I should use to refine the calibration via animal_calibration. Could you please help me?

Other suggestions are welcome! Regarding the image quality, it may not be optimal, but we did our best to have well-lit shots, focus and so on, so I don't think we can do much more in this respect. Actually, we aim to have at least 200-300 openCV charuco detections for each camera pair and most times it works. Manually checking the charuco detections they seem quite ok, thus I guess that the image quality should be good enough.

Thank you in advance for your support, Francesco