Atomic level qubits in silicon are attractive candidates for large-scale quantum computing, however, their quantum properties and controllability are sensitive to details such as the number of donor atoms comprising a qubit and their precise location. This work combines machine learning techniques with million-atom simulations of scanning-tunnelling-microscope (STM) images of dopants to formulate a theoretical framework capable of determining the number of dopants at a particular qubit location and their positions with exact lattice-site precision. A convolutional neural network was trained on 100,000 simulated STM images, acquiring a characterisation fidelity (number and absolute donor positions) of above 98% over a set of 17,600 test images including planar and blurring noise. The method established here will enable a high-precision post-fabrication characterisation of dopant qubits in silicon, with highthroughput potentially alleviating the requirements on the level of resource required for quantum-based characterisation, which may be otherwise a challenge in the context of large qubit arrays for universal quantum computing.Of the leading platforms for the implementation of quantum computing architectures, qubits based on the spin of individual dopant atoms in silicon 1-7 are growing in interest given the nexus with nanoelectronics engineering and the long coherence times 8,9 . For the exchange-based quantum computer design proposals 1,2,10 where the physical separations between atomic qubits are small (10-15 nm), the pathway for scale-up to large two-dimensional arrays generally relies on uniformity of control of qubits and their interactions. Even small variations at the level of one lattice-site for qubits based on single or multiple dopant atoms can significantly affect the design and control of logical operations. While the details of few qubit systems can be determined using electrostatics and electron spin resonance 11 and variations in interactrions mitigated by designing appropriate pulse schemes 12,13 , for large-scale arrays a reliable and fast method of identification (atom count per qubit) and characterisation (exact spatial location of atoms in lattice) is critical. Machine intelligence techniques have been extremely productive in a wide range of applications including material design, medical imaging, and data science, where the design space is enormously large [14][15][16][17] and/or autonomous predictions are required from big data analysis 18 . In quantum devices, the application of deep learning for the automated fabrication of atomic-scale surface defects has been proposed 19,20 . This work integrates the high efficiency of machine learning algorithms towards pattern recognition 21 with multi-million-atom simulations of Scanning-tunnelling microscope (STM) images of donor wave functions 22,23 to formulate a theoretical framework with the capability of high-throughput and automated spatial metrology of the donor qubits in silicon. The ability to pinpoint the donor locations with exact-atom p...