Update scipy / opencv / matplotlib / numpy versions

[jasper-tms]

In d8f4b88 we relaxed the scipy version requirement a bit, but scipy==1.4.1 still only has wheels for python3.8 and below (see available wheels at https://pypi.org/project/scipy/1.4.1/#files). The latest version of scipy currently is 1.13.0, which has wheels for python3.9 to python3.12. We should try just unpinning the scipy version to let pip install the latest version that's compatible with the version of python the user is trying to use. If unpinning breaks things, there might be some work to do to get everything to run with a more modern python version. Maybe aim for 3.10 or so.

This will also fix https://github.com/NeLy-EPFL/DeepFly3D/security/dependabot/2

I can get around to doing this sometime, though @azmaite if you're testing/using this code soon feel free to give the updated scipy a try.