Python

There is no need to use Python virtual environments for this project.

In general the minimum packages you would need for this project are obtained on the Pi by:

apt install git python3-pip python3-picamera python3-numpy python3-h5py

HDF5

HDF5 is a universal, self-describing, compact, lossless, performant data format with easy access from popular programming languages. For example, in Python a 3-D array is written to HDF5 by:

import h5py
import numpy as np

dat = np.random.random((10,100,100))

with h5py.File('mydat.h5', 'w') as f:
    f['dat'] = dat

This HDF5 data is viewable by a wide selection of software, and readable from popular programming languages. For example, from Matlab:

dat = h5read('mydat.h5', 'dat')