While X-ray computed tomography (XCT) is pushed further into the micro- and nanoscale, the limitations of various tool components and object motion become more apparent. For high-resolution XCT, it is necessary but practically difficult to align these tool components with sub-micron precision. The aim is to develop a novel reconstruction methodology that considers unavoidable misalignment and object motion during the data acquisition in order to obtain high-quality three-dimensional images and that is applicable for data recovery from incomplete datasets. A reconstruction software empowered by sophisticated correction modules that autonomously estimates and compensates artefacts using gradient descent and deep learning algorithms has been developed and applied. For motion estimation, a novel computer vision methodology coupled with a deep convolutional neural network approach provides estimates for the object motion by tracking features throughout the adjacent projections. The model is trained using the forward projections of simulated phantoms that consist of several simple geometrical features such as sphere, triangle and rectangular. The feature maps extracted by a neural network are used to detect and to classify features done by a support vector machine. For missing data recovery, a novel deep convolutional neural network is used to infer high-quality reconstruction data from incomplete sets of projections. The forward and back projections of simulated geometric shapes from a range of angular ranges are used to train the model. The model is able to learn the angular dependency based on a limited angle coverage and to propose a new set of projections to suppress artefacts. High-quality three-dimensional images demonstrate that it is possible to effectively suppress artefacts caused by thermomechanical instability of tool components and objects resulting in motion, by center of rotation misalignment and by inaccuracy in the detector position without additional computational efforts. Data recovery from incomplete sets of projections result in directly corrected projections instead of suppressing artefacts in the final reconstructed images. The proposed methodology has been proven and is demonstrated for a ball bearing sample. The reconstruction results are compared to prior corrections and benchmarked with a commercially available reconstruction software. Compared to conventional approaches in XCT imaging and data analysis, the proposed methodology for the generation of high-quality three-dimensional X-ray images is fully autonomous. The methodology presented here has been proven for high-resolution micro-XCT and nano-XCT, however, is applicable for all length scales.