A method for generating improved 3D reconstructions of a sample via slice and view charged particle imaging, the method comprising: acquiring first data relating to a first layer of a sample, the first data having been acquired by the process of: performing a first irradiation of the first layer of the sample with a charged particle beam; and detecting, with a detector system, electrons emitted by the sample resultant from the first irradiation; acquiring second data relating to a second layer of a sample, the second data having been acquired by the process of: performing a second irradiation of the second layer of the sample with the charged particle beam, and detecting, with the detector system, electrons emitted by the sample resultant from the second irradiation; wherein: the first layer of the sample is removed between the first irradiation and the second irradiation; and an electron interaction depth of the charged particle beam is larger than the thickness of the first layer and the thickness of the second layer; enhancing the first data with a training based 3D blind deconvolution algorithm to create enhanced first data, wherein the training based 3D blind deconvolution algorithm reduces blurring caused by first portions of the first data resultant from electron interactions with portions of the sample outside the first layer; enhancing the second data with the training based 3D blind deconvolution algorithm to create enhanced second data, wherein the training based 3D blind deconvolution algorithm reduces blurring caused by second portions of the second data resultant from electron interactions with portions of the sample outside the second layer; and constructing a high-resolution 3D reconstruction of the sample using the enhanced first data and the enhanced second data. performing a first irradiation of the first layer of the sample with a charged particle beam; and detecting, with a detector system, electrons emitted by the sample resultant from the first irradiation; acquiring second data relating to a second layer of a sample, the second data having been acquired by the process of: performing a second irradiation of the second layer of the sample with the charged particle beam, and detecting, with the detector system, electrons emitted by the sample resultant from the second irradiation; wherein: the first layer of the sample is removed between the first irradiation and the second irradiation; and an electron interaction depth of the charged particle beam is larger than the thickness of the first layer and the thickness of the second layer; enhancing the first data with a training based 3D blind deconvolution algorithm to create enhanced first data, wherein the training based 3D blind deconvolution algorithm reduces blurring caused by first portions of the first data resultant from electron interactions with portions of the sample outside the first layer; enhancing the second data with the training based 3D blind deconvolution algorithm to create enhanced second data, wherein the training based 3D blind deconvolution algorithm reduces blurring caused by second portions of the second data resultant from electron interactions with portions of the sample outside the second layer; and constructing a high-resolution 3D reconstruction of the sample using the enhanced first data and the enhanced second data. performing a second irradiation of the second layer of the sample with the charged particle beam, and detecting, with the detector system, electrons emitted by the sample resultant from the second irradiation; wherein: the first layer of the sample is removed between the first irradiation and the second irradiation; and an electron interaction depth of the charged particle beam is larger than the thickness of the first layer and the thickness of the second layer; enhancing the first data with a training based 3D blind deconvolution algorithm to create enhanced first data, wherein the training based 3D blind deconvolution algorithm reduces blurring caused by first portions of the first data resultant from electron interactions with portions of the sample outside the first layer; enhancing the second data with the training based 3D blind deconvolution algorithm to create enhanced second data, wherein the training based 3D blind deconvolution algorithm reduces blurring caused by second portions of the second data resultant from electron interactions with portions of the sample outside the second layer; and constructing a high-resolution 3D reconstruction of the sample using the enhanced first data and the enhanced second data. the first layer of the sample is removed between the first irradiation and the second irradiation; and an electron interaction depth of the charged particle beam is larger than the thickness of the first layer and the thickness of the second layer; enhancing the first data with a training based 3D blind deconvolution algorithm to create enhanced first data, wherein the training based 3D blind deconvolution algorithm reduces blurring caused by first portions of the first data resultant from electron interactions with portions of the sample outside the first layer; enhancing the second data with the training based 3D blind deconvolution algorithm to create enhanced second data, wherein the training based 3D blind deconvolution algorithm reduces blurring caused by second portions of the second data resultant from electron interactions with portions of the sample outside the second layer; and constructing a high-resolution 3D reconstruction of the sample using the enhanced first data and the enhanced second data.