Meshroom VS colmap

Take a look at Meshroom from https://alicevision.org/

It's a pretty decent tool, although not sure if videos work well.

I once tried to build a mesh from an aerial video by extracting certain frames and the result was ok-ish

You'll need to get some practice with photogrammetry or other 3D scanning to get the appropriate shapes for each animal, this should be more or less something the right size with adequate straps and padding - https://alicevision.org is a good place to learn about photogrammetry.

Have you tried Alice Vision? https://alicevision.org

Huh. https://github.com/alicevision/meshroom/issues/1650 suggests you can get the camera positions into blender, and then putting pyramids views in, and then get the interested area.

Another alternative for ptgui is https://alicevision.org and it is free

A new version of Meshroom released last month, so I decided to compare the performance and results of the two with the same dataset and mostly the same settings.

Photogrametrie https://alicevision.org/

Not saying its easy to use, but there is an application gui and it is free: https://github.com/colmap/colmap

Colmap (Model folders (BIN and TXT), dense workspaces, NVM, PLY)

See colmap for example https://colmap.github.io/

You're looking into a problem called photogrammetry, and a well-studied one at that. I'd recommend looking into "shape from motion" (sfm); specifically techniques that do "dense reconstruction." I'd recommend COLMAP to start with. It does pose estimation from images (e.g. you point it at a bunch of images and it will figure out the relative poses of the cameras that took them), as well as sparse and dense reconstcution.

COLMAP builds dense meshes from a collection of cameras https://colmap.github.io/

I’ve seen references to using COLMAP (https://colmap.github.io/) to estimate camera position/pose, e.g. here

Classical photogrammetry, where I agree with u/tdgros that the way to go is https://colmap.github.io/. There are actually better variants in literature but nothing is more reliable and user-friendly than COLMAP. This will give you a very precise point cloud, that can be meshed if needed.